https://netbiolab.org/wiki/api.php?action=feedcontributions&feedformat=atom&user=Ds628
Network Biology Lab - User contributions [en]
2026-05-22T14:35:23Z
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https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3962
Journal Club
2016-08-29T05:27:35Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/10<br />
|style="padding:.4em;"|2016-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=sidespread+parainflammation Widespread parainflammation in human cancer]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/27<br />
|style="padding:.4em;"|2016-22<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27535533 Analysis of protein-coding genetic variation in 60,706 humans]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/20<br />
|style="padding:.4em;"|2016-21<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27322546 Functional characterization of somatic mutations in cancer using network-based inference of protein activity]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/13<br />
|style="padding:.4em;"|2016-20<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=exploiting+single-cell+expression+to+characterize Exploiting single-cell expression to characterize co-expression replicability.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/6<br />
|style="padding:.4em;"|2016-19<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26940869 Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/31<br />
|style="padding:.4em;"|2016-18<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27264179 A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/16<br />
|style="padding:.4em;"|2016-17<br />
|style="padding:.4em;"|JW Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27309802 The landscape of accessible chromatin in mammalian preimplantation embryos]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/8<br />
|style="padding:.4em;"|2016-16<br />
|style="padding:.4em;"|EB Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27064255 Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/1<br />
|style="padding:.4em;"|2016-15<br />
|style="padding:.4em;"|MY Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27040498 Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/25<br />
|style="padding:.4em;"|2016-14<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=integration+of+summary+data+from+gwas+and+eqtl+studies Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/18<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
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|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
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|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3960
Journal Club
2016-08-27T02:45:50Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/27<br />
|style="padding:.4em;"|2016-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://http://www.ncbi.nlm.nih.gov/pubmed/?term=sidespread+parainflammation Widespread parainflammation in human cancer]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/20<br />
|style="padding:.4em;"|2016-21<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://http://www.ncbi.nlm.nih.gov/pubmed/27322546 Functional characterization of somatic mutations in cancer using network-based inference of protein activity]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/13<br />
|style="padding:.4em;"|2016-20<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://http://www.ncbi.nlm.nih.gov/pubmed/27535533 Analysis of protein-coding genetic variation in 60,706 humans]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/6<br />
|style="padding:.4em;"|2016-19<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26940869 Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/31<br />
|style="padding:.4em;"|2016-18<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27264179 A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/16<br />
|style="padding:.4em;"|2016-17<br />
|style="padding:.4em;"|JW Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27309802 The landscape of accessible chromatin in mammalian preimplantation embryos]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/8<br />
|style="padding:.4em;"|2016-16<br />
|style="padding:.4em;"|EB Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27064255 Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/1<br />
|style="padding:.4em;"|2016-15<br />
|style="padding:.4em;"|MY Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27040498 Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/25<br />
|style="padding:.4em;"|2016-14<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=integration+of+summary+data+from+gwas+and+eqtl+studies Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/18<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
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|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3959
Journal Club
2016-08-27T02:42:44Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/27<br />
|style="padding:.4em;"|2016-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://http://www.ncbi.nlm.nih.gov/pubmed/?term=sidespread+parainflammation Widespread parainflammation in human cancer]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/20<br />
|style="padding:.4em;"|2016-21<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://http://www.ncbi.nlm.nih.gov/pubmed/27322546 Functional characterization of somatic mutations in cancer using network-based inference of protein activity]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/13<br />
|style="padding:.4em;"|2016-20<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://http://www.ncbi.nlm.nih.gov/pubmed/27535533 Analysis of protein-coding genetic variation in 60,706 humans]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/6<br />
|style="padding:.4em;"|2016-19<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26940869 Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/30<br />
|style="padding:.4em;"|2016-18<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27264179 A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/16<br />
|style="padding:.4em;"|2016-17<br />
|style="padding:.4em;"|JW Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27309802 The landscape of accessible chromatin in mammalian preimplantation embryos]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/8<br />
|style="padding:.4em;"|2016-16<br />
|style="padding:.4em;"|EB Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27064255 Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/1<br />
|style="padding:.4em;"|2016-15<br />
|style="padding:.4em;"|MY Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27040498 Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/25<br />
|style="padding:.4em;"|2016-14<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=integration+of+summary+data+from+gwas+and+eqtl+studies Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/18<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3958
Journal Club
2016-08-27T02:38:13Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/13<br />
|style="padding:.4em;"|2016-20<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://http://www.ncbi.nlm.nih.gov/pubmed/27535533 Analysis of protein-coding genetic variation in 60,706 humans]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/6<br />
|style="padding:.4em;"|2016-19<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26940869 Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/30<br />
|style="padding:.4em;"|2016-18<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27264179 A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/16<br />
|style="padding:.4em;"|2016-17<br />
|style="padding:.4em;"|JW Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27309802 The landscape of accessible chromatin in mammalian preimplantation embryos]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/8<br />
|style="padding:.4em;"|2016-16<br />
|style="padding:.4em;"|EB Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27064255 Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/1<br />
|style="padding:.4em;"|2016-15<br />
|style="padding:.4em;"|MY Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27040498 Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/25<br />
|style="padding:.4em;"|2016-14<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=integration+of+summary+data+from+gwas+and+eqtl+studies Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/18<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3957
Journal Club
2016-08-27T02:32:25Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/6<br />
|style="padding:.4em;"|2016-19<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26940869 Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/30<br />
|style="padding:.4em;"|2016-18<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27264179 A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/16<br />
|style="padding:.4em;"|2016-17<br />
|style="padding:.4em;"|JW Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27309802 The landscape of accessible chromatin in mammalian preimplantation embryos]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/8<br />
|style="padding:.4em;"|2016-16<br />
|style="padding:.4em;"|EB Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27064255 Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/1<br />
|style="padding:.4em;"|2016-15<br />
|style="padding:.4em;"|MY Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27040498 Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/25<br />
|style="padding:.4em;"|2016-14<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=integration+of+summary+data+from+gwas+and+eqtl+studies Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/18<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
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[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
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|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
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[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
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|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
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[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
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|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
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|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
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[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
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|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
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[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
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|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
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|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
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[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
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|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3948
Journal Club
2016-08-08T02:41:55Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/22<br />
|style="padding:.4em;"|2016-18<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27264179 A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/16<br />
|style="padding:.4em;"|2016-17<br />
|style="padding:.4em;"|JW Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27309802 The landscape of accessible chromatin in mammalian preimplantation embryos]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/8<br />
|style="padding:.4em;"|2016-16<br />
|style="padding:.4em;"|EB Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27064255 Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/1<br />
|style="padding:.4em;"|2016-15<br />
|style="padding:.4em;"|MY Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27040498 Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/25<br />
|style="padding:.4em;"|2016-14<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=integration+of+summary+data+from+gwas+and+eqtl+studies Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/18<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=People&diff=3942
People
2016-08-02T06:36:28Z
<p>Ds628: /* Principal Investigator */</p>
<hr />
<div>__NOTOC__<br />
=='''Principal Investigator'''==<br />
{|border="0" width="150"<br />
|align="center"|[[File:이인석-2011사진.jpg|77px|link=people:IS_Lee]]<br />
|-<br />
|align="center"|[[people:IS_Lee|Insuk Lee]]<br />
|-<br />
|}<br />
<br />
=='''Research Professor/Postdoc Fellow/Staff Scientist'''==<br />
{|border="0" width="300"<br />
|align="center"|[[File:People_JE_Shim_EDIT.JPG|70px|link=people:JE_Shim]]<br />
|align="center"|[[File:SYLee.jpg|70px|link=people:SY_Lee]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Jung Eun Shim]]<br />
|align="center"|[[people:SY_Lee|Sangyoung Lee]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Research Professor]]<br />
|align="center"|[[people:SY_Lee|Research Assistant]]<br />
|}<br />
<br />
=='''Graduate Students'''==<br />
{|border="0" width="1000"<br />
|align="center" |[[File:Banmyungham.JPG|70px|link=people:ER_Kim]]<br />
|align="center" |[[File:Tak_sajin3.jpg|70px|link=people:T_Lee]]<br />
|align="center" |[[File:heonjong.jpg|70px|link=people:HJ_Han]]<br />
|align="center" |[[File:People_KSKim.jpg|70px|link=people:KS_Kim]]<br />
|align="center"|[[File:Smyang.jpg|70px|link=people:SM_Yang]]<br />
|align="center"|[[File:배다솜.jpg|70px|link=People:DS Bae]]<br />
|align="center"|[[File:CY KIM.jpg|70px|link=People:CY_Kim]]<br />
|align="center"|[[File:Muyoung_Lee_2.jpg|70px|link=People:M_Lee]]<br />
|align="center"|[[File:Cho_JW.png|70px|link=People:J_Cho]]<br />
|align="center"|[[File:kim_EB.jpg|70px|link=People:E_Kim]]<br />
|-<br />
|align="center"|[[people:ER_Kim|Eiru Kim]]<br />
|align="center"|[[people:T_Lee|Tak Lee]]<br />
|align="center"|[[people:HJ_Han|Heon Jong Han]]<br />
|align="center"|[[people:KS_Kim|Kyungsoo Kim]]<br />
|align="center"|[[people:SM_Yang|Sunmo Yang]]<br />
|align="center"|[[People:DS Bae|Dasom Bae]]<br />
|align="center"|[[People:CY Kim|Chan Yeong Kim]]<br />
|align="center"|[[People:M_Lee|Muyoung Lee]]<br />
|align="center"|[[People:J_Cho|Jaewon Cho]]<br />
|align="center"|[[People:E_Kim|Eunbeen Kim]]<br />
|-<br />
|align="center"|[[people:ER_Kim|PhD candidate]]<br />
|align="center"|[[people:T_Lee|PhD candidate]]<br />
|align="center"|[[People:HJ_Han|PhD candidate]]<br />
|align="center"|[[people:KS_Kim|PhD candidate]]<br />
|align="center"|[[people:SM_Yang|M.Eng. course/System Admin]]<br />
|align="center"|[[people:DS Bae|PhD course]]<br />
|align="center"|[[people:CY Kim|PhD course]]<br />
|align="center"|[[people:M_Lee|PhD course]]<br />
|align="center"|[[people:J_Cho|PhD course]]<br />
|align="center"|[[people:E_Kim|M.Eng course]]<br />
|}<br />
<br />
=='''Undergraduate Students'''==<br />
*Sungho Lee<br />
*Yaeji Kim<br />
*Changbae Bang<br />
*Seoyoung Choi<br />
*Aejoo Hong<br />
<br />
=='''Visiting scientists/students'''==<br />
<br />
<br />
=='''Alumni'''==<br />
*Former Post-docs and Staff Scientists<br />
**Taeyun Oh (2009.5-2011.12), current position: Deputy Principal Consultant, INSILICOGEN (www.insilicogen.com) <br />
**Samuel Beck (2011.2-2011.12), current position; Postdoc fellow, University of Texas at Austin [http://web.biosci.utexas.edu/kimlab/ Jonghwan Kim's Lab]<br />
**Jawon Song (2011.1-2012.5), current position; Research Scientist, Texas Advanced Computing Center, Austin, TX, USA<br />
**Yoonhee Ko (2012.8-2014.2), current position; Fellow, Severance Medical center (Yonsei Medical school)<br />
**Jonghoon Lee (2013.10-2014.2), current position; Assistant Professor, CHA Medical school <br />
**Sohyun Hwang (2010.3-2015.8), current position; Research Professor, Ewha Womans University<br />
<br />
*Former Graduate Students<br />
**Sun-Gou Ji (2009.9-2011.8), M.Eng.; current position; Research Associate, Sanger Genome Institute, UK<br />
**Junha Shin (2008.9-2014.2), PhD; <br />
**Hanhae Kim (2008.9-2015.2), PhD; current position; Associate Research Fellow, Korea Institute of S&T Evaluation and Planning (KISTEP)<br />
**Ara Cho (2008.9-2015.2), PhD; Postdoc fellow, UCSF, [http://diazlab.ucsf.edu/ Diaz Lab]<br />
**Hyojin Kim (2013.3-2015.2), M.Eng.; current position; Research Assistant, Samsung Advanced Institute for Health Sciences & Technology (SAIHST)<br />
**Hongseok Shim (2013.9-2015.8), M.Eng.; <br />
<br />
*Former Visiting Scientists/Students<br />
**Minkyung Shin (2012.3-2012.7), went to a graduate school, University of Southern California, USA<br />
**Paul Chung (2012 summer high school student intern), went to University of Pennsylvania (Bio Engineering) <br />
**Susie Shin (2013 summer high school student intern), went to Vanderbilt University (Bio Engineering)<br />
**Hyunjin Cho (Johns Hopkins University, Bioinformatics)<br />
<br />
*Former Undergraduate Students<br />
**Ila Shin, went to a medical school (Yonsei Univ.)<br />
**Yoonkyung Ko<br />
**Sangyo Park, went to a law school (Kyounghee Univ.)<br />
**Jayoon Shin, went to a medical school (Pusan National Univ.)<br />
**Dongjoo Sun, went to a dental school (Wongwang Univ.)<br />
**Eulsoo Kim<br />
**Myungwhan Lee, went to a medical school (Yonsei Univ.)<br />
**Moonhee Lee, went to a graduate school, University of Amsterdam, Netherlands<br />
**Jinhyun Ju, went to a graduate school, Cornell Medical School, NY, USA (Research field: Computational Systems Biology)<br />
**Haeyoung Shin, went to a graduate school, Brown University, USA (Research field: Computational Neuroscience)<br />
**Joonghee Soh, went to a graduate school, KAIST, Korea (Research field: Culture Technology)<br />
**Hee Jung Cho, went to a graduate school, UC Berkeley <br />
**TaeHwan Kim, went to a medical school<br />
**Joohyung Kim, went to a medical school (Kyungpook National Univ.)<br />
**Donghyun Shin, went to a medical school (Yonsei Univ.)<br />
**Sunphil Kim<br />
**Jaeho Shim<br />
**Seunghyun Shin</div>
Ds628
https://netbiolab.org/wiki/index.php?title=File:%EC%9D%B4%EC%9D%B8%EC%84%9D-2011%EC%82%AC%EC%A7%84.jpg&diff=3941
File:이인석-2011사진.jpg
2016-08-02T06:36:04Z
<p>Ds628: </p>
<hr />
<div></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Welcome_to_Network_Biology_Laboratory&diff=3938
Welcome to Network Biology Laboratory
2016-08-02T02:00:57Z
<p>Ds628: /* Oral Presentation */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
|rowspan="2" style="padding-right:20px;"|<br />
[[File :P4070576 2.jpg|580px|center|middle|Main Photo]]<br />
<br />
|colspan=2|<br />
=== Research Keyword Cloud ===<br />
<div>{{#widget:AddHtml|content=<img src="../wiki/cloud.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div><br />
|-<br />
|<br />
=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| JE Shim<br />
|style="width:65px"| T Lee<br />
|style="width:65px"| HJ Han<br />
|-<br />
| KS Kim<br />
| ER Kim<br />
| CY Kim<br />
|-<br />
| DS Bae<br />
| SM Yang<br />
| MY Lee*<br />
|-<br />
| JW Cho<br />
| EB Kim<br />
| <br />
|}<br />
|<br />
<br />
=== Visitors Trend ===<br />
[https://www.clustrmaps.com/map/Netbiolab.org https://www.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]<br />
|-<br />
|colspan=3|<br />
===Contact Informations===<br />
<pre><br />
Yonsei University 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea <br />
Office: Engineering Research Park B118DA<br />
+82-70-8625-5205 <br />
</pre><br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=Welcome_to_Network_Biology_Laboratory&diff=3937
Welcome to Network Biology Laboratory
2016-08-02T02:00:42Z
<p>Ds628: /* Oral Presentation */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
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[[File :P4070576 2.jpg|580px|center|middle|Main Photo]]<br />
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|colspan=2|<br />
=== Research Keyword Cloud ===<br />
<div>{{#widget:AddHtml|content=<img src="../wiki/cloud.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div><br />
|-<br />
|<br />
=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| JE Shim<br />
|style="width:65px"| T Lee<br />
|style="width:65px"| HJ Han<br />
|-<br />
| KS Kim<br />
| ER Kim<br />
| CY Kim<br />
|-<br />
| DS Bae<br />
| SM Yang*<br />
| MY Lee*<br />
|-<br />
| JW Cho<br />
| EB Kim<br />
| <br />
|}<br />
|<br />
<br />
=== Visitors Trend ===<br />
[https://www.clustrmaps.com/map/Netbiolab.org https://www.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]<br />
|-<br />
|colspan=3|<br />
===Contact Informations===<br />
<pre><br />
Yonsei University 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea <br />
Office: Engineering Research Park B118DA<br />
+82-70-8625-5205 <br />
</pre><br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=Welcome_to_Network_Biology_Laboratory&diff=3936
Welcome to Network Biology Laboratory
2016-08-02T02:00:13Z
<p>Ds628: /* Oral Presentation */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
|rowspan="2" style="padding-right:20px;"|<br />
[[File :P4070576 2.jpg|580px|center|middle|Main Photo]]<br />
<br />
|colspan=2|<br />
=== Research Keyword Cloud ===<br />
<div>{{#widget:AddHtml|content=<img src="../wiki/cloud.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div><br />
|-<br />
|<br />
=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| JE Shim<br />
|style="width:65px"| T Lee<br />
|style="width:65px"| HJ Han<br />
|-<br />
| KS Kim<br />
| ER Kim<br />
| CY Kim<br />
|-<br />
| DS Bae<br />
| SM Yang*<br />
| MY Lee*<br />
|-<br />
| JW Lee<br />
| EB Kim<br />
| <br />
|}<br />
|<br />
<br />
=== Visitors Trend ===<br />
[https://www.clustrmaps.com/map/Netbiolab.org https://www.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]<br />
|-<br />
|colspan=3|<br />
===Contact Informations===<br />
<pre><br />
Yonsei University 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea <br />
Office: Engineering Research Park B118DA<br />
+82-70-8625-5205 <br />
</pre><br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:E_Kim&diff=3922
People:E Kim
2016-07-14T06:44:58Z
<p>Ds628: /* Kim Eunbeen */</p>
<hr />
<div>===Kim Eunbeen===<br />
{|<br />
|[[File:Kim_EB.jpg|300px]]<br />
|'''PhD program student'''(2016~) Department of Biotechnology, Yonsei University<br />
(2011-2016) Department of Bio medical engineering, Korea University<br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:J_Cho&diff=3921
People:J Cho
2016-07-14T06:44:09Z
<p>Ds628: /* Cho Jaewan */</p>
<hr />
<div>===Cho Jaewan===<br />
{|<br />
|[[File:Cho_JW.png|300px]]<br />
|'''Ph.D program student'''(2016~) Department of Biotechnology, Yonsei University<br />
'''M.S'''(2014-2016) Department of Chemistry, Yonsei University<br />
<br />
(2008-2014) Department of Chemistry, Yonsei University<br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=Welcome_to_Network_Biology_Laboratory&diff=3920
Welcome to Network Biology Laboratory
2016-07-14T06:40:55Z
<p>Ds628: /* Oral Presentation */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
|rowspan="2" style="padding-right:20px;"|<br />
[[File :P4070576 2.jpg|580px|center|middle|Main Photo]]<br />
<br />
|colspan=2|<br />
=== Research Keyword Cloud ===<br />
<div>{{#widget:AddHtml|content=<img src="../wiki/cloud.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div><br />
|-<br />
|<br />
=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| JE Shim<br />
|style="width:65px"| T Lee<br />
|style="width:65px"| HJ Han<br />
|-<br />
| KS Kim<br />
| ER Kim<br />
| CY Kim<br />
|-<br />
| DS Bae<br />
| SM Yang*<br />
| MY Lee<br />
|}<br />
|<br />
<br />
=== Visitors Trend ===<br />
[https://www.clustrmaps.com/map/Netbiolab.org https://www.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]<br />
|-<br />
|colspan=3|<br />
===Contact Informations===<br />
<pre><br />
Yonsei University 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea <br />
Office: Engineering Research Park B118DA<br />
+82-70-8625-5205 <br />
</pre><br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3915
Journal Club
2016-07-08T01:03:10Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/29<br />
|style="padding:.4em;"|2016-18<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27264179 A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/22<br />
|style="padding:.4em;"|2016-17<br />
|style="padding:.4em;"|JW Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27309802 The landscape of accessible chromatin in mammalian preimplantation embryos]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/8<br />
|style="padding:.4em;"|2016-16<br />
|style="padding:.4em;"|EB Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27064255 Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/1<br />
|style="padding:.4em;"|2016-15<br />
|style="padding:.4em;"|MY Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27259156 Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/25<br />
|style="padding:.4em;"|2016-14<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=integration+of+summary+data+from+gwas+and+eqtl+studies Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/18<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3914
Journal Club
2016-07-07T06:04:14Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/22<br />
|style="padding:.4em;"|2016-18<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27264179 A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/8<br />
|style="padding:.4em;"|2016-17<br />
|style="padding:.4em;"|EB Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27064255 Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/1<br />
|style="padding:.4em;"|2016-16<br />
|style="padding:.4em;"|JW Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27309802 The landscape of accessible chromatin in mammalian preimplantation embryos]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/25<br />
|style="padding:.4em;"|2016-15<br />
|style="padding:.4em;"|MY Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27259156 Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/18<br />
|style="padding:.4em;"|2016-14<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=integration+of+summary+data+from+gwas+and+eqtl+studies Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/11<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3913
Journal Club
2016-07-07T06:03:36Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/22<br />
|style="padding:.4em;"|2016-18<br />
|style="padding:.4em;"DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27264179 A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/8<br />
|style="padding:.4em;"|2016-17<br />
|style="padding:.4em;"EB Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27064255 Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/1<br />
|style="padding:.4em;"|2016-16<br />
|style="padding:.4em;"JW Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27309802 The landscape of accessible chromatin in mammalian preimplantation embryos]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/25<br />
|style="padding:.4em;"|2016-15<br />
|style="padding:.4em;"MY Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27259156 Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/18<br />
|style="padding:.4em;"|2016-14<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=integration+of+summary+data+from+gwas+and+eqtl+studies Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/11<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3912
Journal Club
2016-07-07T05:55:56Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/18<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=integration+of+summary+data+from+gwas+and+eqtl+studies Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/11<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
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|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3911
Journal Club
2016-07-07T05:53:58Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/11<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3910
Journal Club
2016-07-07T05:50:36Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3909
Journal Club
2016-07-07T05:43:04Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/7/11<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3908
Journal Club
2016-07-07T05:40:48Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/7/11<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3907
Journal Club
2016-07-07T05:38:18Z
<p>Ds628: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Ds628
https://netbiolab.org/wiki/index.php?title=People&diff=3902
People
2016-06-30T06:41:01Z
<p>Ds628: /* Graduate Students */</p>
<hr />
<div>__NOTOC__<br />
=='''Principal Investigator'''==<br />
{|border="0" width="150"<br />
|align="center"|[[File:People_ISLee_03.jpg|77px|link=people:IS_Lee]]<br />
|-<br />
|align="center"|[[people:IS_Lee|Insuk Lee]]<br />
|-<br />
|}<br />
<br />
=='''Research Professor/Postdoc Fellow/Staff Scientist'''==<br />
{|border="0" width="300"<br />
|align="center"|[[File:People_JE_Shim_EDIT.JPG|70px|link=people:JE_Shim]]<br />
|align="center"|[[File:SYLee.jpg|70px|link=people:SY_Lee]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Jung Eun Shim]]<br />
|align="center"|[[people:SY_Lee|Sangyoung Lee]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Research Professor]]<br />
|align="center"|[[people:SY_Lee|Research Assistant]]<br />
|}<br />
<br />
=='''Graduate Students'''==<br />
{|border="0" width="1000"<br />
|align="center" |[[File:Banmyungham.JPG|70px|link=people:ER_Kim]]<br />
|align="center" |[[File:Tak_sajin3.jpg|70px|link=people:T_Lee]]<br />
|align="center" |[[File:heonjong.jpg|70px|link=people:HJ_Han]]<br />
|align="center" |[[File:People_KSKim.jpg|70px|link=people:KS_Kim]]<br />
|align="center"|[[File:Smyang.jpg|70px|link=people:SM_Yang]]<br />
|align="center"|[[File:배다솜.jpg|70px|link=People:DS Bae]]<br />
|align="center"|[[File:CY KIM.jpg|70px|link=People:CY_Kim]]<br />
|align="center"|[[File:Muyoung_Lee_2.jpg|70px|link=People:M_Lee]]<br />
|align="center"|[[File:Cho_JW.png|70px|link=People:J_Cho]]<br />
|align="center"|[[File:kim_EB.jpg|70px|link=People:E_Kim]]<br />
|-<br />
|align="center"|[[people:ER_Kim|Eiru Kim]]<br />
|align="center"|[[people:T_Lee|Tak Lee]]<br />
|align="center"|[[people:HJ_Han|Heon Jong Han]]<br />
|align="center"|[[people:KS_Kim|Kyungsoo Kim]]<br />
|align="center"|[[people:SM_Yang|Sunmo Yang]]<br />
|align="center"|[[People:DS Bae|Dasom Bae]]<br />
|align="center"|[[People:CY Kim|Chan Yeong Kim]]<br />
|align="center"|[[People:M_Lee|Muyoung Lee]]<br />
|align="center"|[[People:J_Cho|Jaewon Cho]]<br />
|align="center"|[[People:E_Kim|Eunbeen Kim]]<br />
|-<br />
|align="center"|[[people:ER_Kim|PhD candidate]]<br />
|align="center"|[[people:T_Lee|PhD candidate]]<br />
|align="center"|[[People:HJ_Han|PhD course]]<br />
|align="center"|[[people:KS_Kim|PhD course]]<br />
|align="center"|[[people:SM_Yang|M.Eng. course/System Admin]]<br />
|align="center"|[[people:DS Bae|PhD course]]<br />
|align="center"|[[people:CY Kim|PhD course]]<br />
|align="center"|[[people:M_Lee|PhD course]]<br />
|align="center"|[[people:J_Cho|PhD course]]<br />
|align="center"|[[people:E_Kim|PhD course]]<br />
|}<br />
<br />
=='''Undergraduate Students'''==<br />
<br />
<br />
=='''Visiting scientists/students'''==<br />
<br />
<br />
=='''Alumni'''==<br />
*Former Post-docs and Staff Scientists<br />
**Taeyun Oh (2009.5-2011.12), current position: Deputy Principal Consultant, INSILICOGEN (www.insilicogen.com) <br />
**Samuel Beck (2011.2-2011.12), current position; Postdoc fellow, University of Texas at Austin [http://web.biosci.utexas.edu/kimlab/ Jonghwan Kim's Lab]<br />
**Jawon Song (2011.1-2012.5), current position; Research Scientist, Texas Advanced Computing Center, Austin, TX, USA<br />
**Yoonhee Ko (2012.8-2014.2), current position; Fellow, Severance Medical center (Yonsei Medical school)<br />
**Jonghoon Lee (2013.10-2014.2), current position; Assistant Professor, CHA Medical school <br />
**Sohyun Hwang (2010.3-2015.8), current position; Research Professor, Ewha Womans University<br />
<br />
*Former Graduate Students<br />
**Sungou Ji (2009.9-2011.8), M.Eng.; current position; Postdoc fellow, Sanger Genome Institute, Cambridge University, UK (Research field: Statistical Genomics)<br />
**Junha Shin (2008.9-2014.2), PhD; <br />
**Hanhae Kim (2008.9-2015.2), PhD; current position; Associate Research Fellow, Korea Institute of S&T Evaluation and Planning (KISTEP)<br />
**Ara Cho (2008.9-2015.2), PhD; <br />
**Hyojin Kim (2013.3-2015.2), M.Eng.; current position; Research Assistant, Samsung Advanced Institute for Health Sciences & Technology (SAIHST)<br />
**Hongseok Shim (2013.9-2015.8), M.Eng.; <br />
<br />
*Former Visiting Scientists/Students<br />
**Minkyung Shin (2012.3-2012.7), went to a graduate school, University of Southern California, USA<br />
**Paul Chung (2012 summer high school student intern), went to University of Pennsylvania (Bio Engineering) <br />
**Susie Shin (2013 summer high school student intern), went to Vanderbilt University (Bio Engineering)<br />
**Hyunjin Cho (Johns Hopkins University, Bioinformatics)<br />
<br />
*Former Undergraduate Students<br />
**Ila Shin, went to a medical school (Yonsei Univ.)<br />
**Yoonkyung Ko<br />
**Sangyo Park, went to a law school (Kyounghee Univ.)<br />
**Jayoon Shin, went to a medical school (Pusan National Univ.)<br />
**Dongjoo Sun, went to a dental school (Wongwang Univ.)<br />
**Eulsoo Kim<br />
**Myungwhan Lee, went to a medical school (Yonsei Univ.)<br />
**Moonhee Lee, went to a graduate school, University of Amsterdam, Netherlands<br />
**Jinhyun Ju, went to a graduate school, Cornell Medical School, NY, USA (Research field: Computational Systems Biology)<br />
**Haeyoung Shin, went to a graduate school, Brown University, USA (Research field: Computational Neuroscience)<br />
**Joonghee Soh, went to a graduate school, KAIST, Korea (Research field: Culture Technology)<br />
**Hee Jung Cho, went to a graduate school, UC Berkeley <br />
**TaeHwan Kim, went to a medical school<br />
**Joohyung Kim, went to a medical school (Kyungpook National Univ.)<br />
**Donghyun Shin, went to a medical school (Yonsei Univ.)<br />
**Sunphil Kim<br />
**Jaeho Shim<br />
**Seunghyun Shin</div>
Ds628
https://netbiolab.org/wiki/index.php?title=Welcome_to_Network_Biology_Laboratory&diff=3870
Welcome to Network Biology Laboratory
2016-06-11T01:17:27Z
<p>Ds628: /* Oral Presentation */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
|rowspan="2" style="padding-right:20px;"|<br />
[[File :P4070576 2.jpg|580px|center|middle|Main Photo]]<br />
<br />
|colspan=2|<br />
=== Research Keyword Cloud ===<br />
<div>{{#widget:AddHtml|content=<img src="../wiki/cloud.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div><br />
|-<br />
|<br />
=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| JE Shim<br />
|style="width:65px"| T Lee<br />
|style="width:65px"| HJ Han<br />
|-<br />
| KS Kim<br />
| ER Kim<br />
| CY Kim*<br />
|-<br />
| DS Bae<br />
| SM Yang<br />
| MY Lee<br />
|}<br />
|<br />
<br />
=== Visitors Trend ===<br />
[http://www2.clustrmaps.com/user/563d3fa7 http://www2.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]<br />
|-<br />
|colspan=3|<br />
===Contact Informations===<br />
<pre><br />
Yonsei University 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea <br />
Office: Engineering Research Park B118DA<br />
+82-70-8625-5205 <br />
</pre><br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:J_Cho&diff=3869
People:J Cho
2016-06-11T01:16:34Z
<p>Ds628: /* Cho Jaewan */</p>
<hr />
<div>===Cho Jaewan===<br />
{|<br />
|[[File:Cho_JW.png|300px]]<br />
|'''Ph.D program student'''(2016~) Department of Biotechnology, Yonsei University<br />
'''M.S'''(2014-2016) Department of Chemistry, Yonsei University<br />
(2008-2014) Department of Chemistry, Yonsei University<br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:J_Cho&diff=3868
People:J Cho
2016-06-11T01:15:01Z
<p>Ds628: /* Cho Jaewan */</p>
<hr />
<div>===Cho Jaewan===<br />
{|<br />
|[[File:Cho_JW.png|300px]]<br />
|'''Ph.D program student'''(2016~) Department of Biotechnology, Yonsei University<br />
'''MS'''(2014-2016) Department of Chemistry, Yonsei University<br />
(2008-2014) Department of Chemistry, Yonsei University<br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People&diff=3866
People
2016-06-08T06:39:47Z
<p>Ds628: </p>
<hr />
<div>__NOTOC__<br />
=='''Principal Investigator'''==<br />
{|border="0" width="150"<br />
|align="center"|[[File:People_ISLee_03.jpg|77px|link=people:IS_Lee]]<br />
|-<br />
|align="center"|[[people:IS_Lee|Insuk Lee]]<br />
|-<br />
|}<br />
<br />
=='''Research Professor/Postdoc Fellow/Staff Scientist'''==<br />
{|border="0" width="300"<br />
|align="center"|[[File:People_JE_Shim_EDIT.JPG|70px|link=people:JE_Shim]]<br />
|align="center"|[[File:SYLee.jpg|70px|link=people:SY_Lee]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Jung Eun Shim]]<br />
|align="center"|[[people:SY_Lee|Sangyoung Lee]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Research Professor]]<br />
|align="center"|[[people:SY_Lee|Research Assistant]]<br />
|}<br />
<br />
=='''Graduate Students'''==<br />
{|border="0" width="900"<br />
|align="center" |[[File:Banmyungham.JPG|70px|link=people:ER_Kim]]<br />
|align="center" |[[File:Tak_sajin3.jpg|70px|link=people:T_Lee]]<br />
|align="center" |[[File:heonjong.jpg|70px|link=people:HJ_Han]]<br />
|align="center" |[[File:People_KSKim.jpg|70px|link=people:KS_Kim]]<br />
|align="center"|[[File:Smyang.jpg|70px|link=people:SM_Yang]]<br />
|align="center"|[[File:배다솜.jpg|70px|link=People:DS Bae]]<br />
|align="center"|[[File:CY KIM.jpg|70px|link=People:CY_Kim]]<br />
|align="center"|[[File:Muyoung_Lee_2.jpg|70px|link=People:M_Lee]]<br />
|align="center"|[[File:Cho_JW.png|70px|link=People:J_Cho]]<br />
|align="center"|[[File:kim_EB.jpg|70px|link=People:E_Kim]]<br />
|-<br />
|align="center"|[[people:ER_Kim|Eiru Kim]]<br />
|align="center"|[[people:T_Lee|Tak Lee]]<br />
|align="center"|[[people:HJ_Han|Heon Jong Han]]<br />
|align="center"|[[people:KS_Kim|Kyungsoo Kim]]<br />
|align="center"|[[people:SM_Yang|Sunmo Yang]]<br />
|align="center"|[[People:DS Bae|Dasom Bae]]<br />
|align="center"|[[People:CY Kim|Chan Yeong Kim]]<br />
|align="center"|[[People:M_Lee|Muyoung Lee]]<br />
|align="center"|[[People:J_Cho|Jaewan Cho]]<br />
|align="center"|[[People:E_Kim|Eunbeen Kim]]<br />
|-<br />
|align="center"|[[people:ER_Kim|PhD candidate]]<br />
|align="center"|[[people:T_Lee|PhD candidate]]<br />
|align="center"|[[People:HJ_Han|PhD course]]<br />
|align="center"|[[people:KS_Kim|PhD course]]<br />
|align="center"|[[people:SM_Yang|MS course/System Admin]]<br />
|align="center"|[[people:DS Bae|PhD course]]<br />
|align="center"|[[people:CY Kim|PhD course]]<br />
|align="center"|[[people:M_Lee|PhD course]]<br />
|align="center"|[[people:J_Cho|PhD course]]<br />
|align="center"|[[people:E_Kim|MS course]]<br />
|}<br />
<br />
=='''Undergraduate Students'''==<br />
<br />
<br />
=='''Visiting scientists/students'''==<br />
<br />
<br />
=='''Alumni'''==<br />
*Former Post-docs and Staff Scientists<br />
**Taeyun Oh (2009.5-2011.12), current position: Deputy Principal Consultant, INSILICOGEN (www.insilicogen.com) <br />
**Samuel Beck (2011.2-2011.12), current position; Postdoc fellow, University of Texas at Austin (Jonghwan Kim's Lab)<br />
**Jawon Song (2011.1-2012.5), current position; Research Scientist, Texas Advanced Computing Center, Austin, TX, USA<br />
**Yoonhee Ko (2012.8-2014.2), current position; Fellow, Severance Medical center (Yonsei Medical school)<br />
**Jonghoon Lee (2013.10-2014.2), current position; Assistant Professor, CHA Medical school <br />
**Sohyun Hwang (2010.3-2015.8), current position; Research Professor, Ewha Womans University<br />
<br />
*Former Graduate Students<br />
**Sungou Ji (2009.9-2011.8), MS; current position; Postdoc fellow, Sanger Genome Institute, Cambridge University, UK (Research field: Statistical Genomics)<br />
**Junha Shin (2008.9-2014.2), PhD; <br />
**Hanhae Kim (2008.9-2015.2), PhD; current position; Associate Research Fellow, Korea Institute of S&T Evaluation and Planning (KISTEP)<br />
**Ara Cho (2008.9-2015.2), PhD; <br />
**Hyojin Kim (2013.3-2015.2), MS; current position; Research Assistant, Samsung Advanced Institute for Health Sciences & Technology (SAIHST)<br />
**Hongseok Shim (2013.9-2015.8), MS; <br />
<br />
*Former Visiting Scientists/Students<br />
**Minkyung Shin (2012.3-2012.7), went to a graduate school, University of Southern California, USA<br />
**Paul Chung (2012 summer high school student intern), went to University of Pennsylvania (Bio Engineering) <br />
**Susie Shin (2013 summer high school student intern), went to Vanderbilt University (Bio Engineering)<br />
**Hyunjin Cho (Johns Hopkins University, Bioinformatics)<br />
<br />
*Former Undergraduate Students<br />
**Ila Shin, went to a medical school (Yonsei Univ.)<br />
**Yoonkyung Ko<br />
**Sangyo Park, went to a law school (Kyounghee Univ.)<br />
**Jayoon Shin, went to a medical school (Pusan National Univ.)<br />
**Dongjoo Sun, went to a dental school (Wongwang Univ.)<br />
**Eulsoo Kim<br />
**Myungwhan Lee, went to a medical school (Yonsei Univ.)<br />
**Moonhee Lee, went to a graduate school, University of Amsterdam, Netherlands<br />
**Jinhyun Ju, went to a graduate school, Cornell Medical School, NY, USA (Research field: Computational Systems Biology)<br />
**Haeyoung Shin, went to a graduate school, Brown University, USA (Research field: Computational Neuroscience)<br />
**Joonghee Soh, went to a graduate school, KAIST, Korea (Research field: Culture Technology)<br />
**Hee Jung Cho, went to a graduate school, UC Berkeley <br />
**TaeHwan Kim, went to a medical school<br />
**Joohyung Kim, went to a medical school (Kyungpook National Univ.)<br />
**Donghyun Shin, went to a medical school (Yonsei Univ.)<br />
**Sunphil Kim<br />
**Jaeho Shim<br />
**Seunghyun Shin</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:E_Kim&diff=3865
People:E Kim
2016-06-08T06:34:34Z
<p>Ds628: Created page with "===Kim Eunbeen=== {| |300px |'''MS program student'''(2016~) Department of Biotechnology, Yonsei University (2011-2016) Department of Bio medical engineeri..."</p>
<hr />
<div>===Kim Eunbeen===<br />
{|<br />
|[[File:Kim_EB.jpg|300px]]<br />
|'''MS program student'''(2016~) Department of Biotechnology, Yonsei University<br />
(2011-2016) Department of Bio medical engineering, Korea University<br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:J_Cho&diff=3864
People:J Cho
2016-06-08T06:32:09Z
<p>Ds628: /* Cho Jaewan */</p>
<hr />
<div>===Cho Jaewan===<br />
{|<br />
|[[File:Cho_JW.png|300px]]<br />
|'''Ph.D program student'''(2016~) Department of Biotechnology, Yonsei University<br />
(2014-2016) Department of Chemistry, Yonsei University<br />
(2008-2014) Department of Chemistry, Yonsei University<br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:J_Cho&diff=3863
People:J Cho
2016-06-08T06:30:18Z
<p>Ds628: /* Cho Jaewan */</p>
<hr />
<div>===Cho Jaewan===<br />
{|<br />
|[[File:Cho_JW.png|300px]]<br />
|'''Ph.D program student'''(2016~) Department of Biotechnology, Yonsei University<br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:J_Cho&diff=3862
People:J Cho
2016-06-08T06:29:46Z
<p>Ds628: /* Cho Jaewan */</p>
<hr />
<div>===Cho Jaewan===<br />
{|<br />
|[[File:Cho_JW.jpg|300px]]<br />
|'''Ph.D program student'''(2016~) Department of Biotechnology, Yonsei University<br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:J_Cho&diff=3861
People:J Cho
2016-06-08T06:28:55Z
<p>Ds628: </p>
<hr />
<div>===Cho Jaewan===<br />
{|<br />
|[[File:J_Cho.jpg|300px]]<br />
|'''Ph.D program student'''(2016~) Department of Biotechnology, Yonsei University<br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:J_Cho&diff=3860
People:J Cho
2016-06-08T06:28:22Z
<p>Ds628: Created page with "===Muyoung Lee=== {| |300px |'''Ph.D program student'''(2016~) Department of Biotechnology, Yonsei University |}"</p>
<hr />
<div>===Muyoung Lee===<br />
{|<br />
|[[File:jw_Cho.jpg|300px]]<br />
|'''Ph.D program student'''(2016~) Department of Biotechnology, Yonsei University<br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People&diff=3859
People
2016-06-08T06:26:16Z
<p>Ds628: /* Graduate Students */</p>
<hr />
<div>__NOTOC__<br />
=='''Principal Investigator'''==<br />
{|border="0" width="150"<br />
|align="center"|[[File:People_ISLee_03.jpg|77px|link=people:IS_Lee]]<br />
|-<br />
|align="center"|[[people:IS_Lee|Insuk Lee]]<br />
|-<br />
|}<br />
<br />
=='''Research Professor/Postdoc Fellow/Staff Scientist'''==<br />
{|border="0" width="300"<br />
|align="center"|[[File:People_JE_Shim_EDIT.JPG|70px|link=people:JE_Shim]]<br />
|align="center"|[[File:SYLee.jpg|70px|link=people:SY_Lee]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Jung Eun Shim]]<br />
|align="center"|[[people:SY_Lee|Sangyoung Lee]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Research Professor]]<br />
|align="center"|[[people:SY_Lee|Research Assistant]]<br />
|}<br />
<br />
=='''Graduate Students'''==<br />
{|border="0" width="900"<br />
|align="center" |[[File:Banmyungham.JPG|70px|link=people:ER_Kim]]<br />
|align="center" |[[File:Tak_sajin3.jpg|70px|link=people:T_Lee]]<br />
|align="center" |[[File:heonjong.jpg|70px|link=people:HJ_Han]]<br />
|align="center" |[[File:People_KSKim.jpg|70px|link=people:KS_Kim]]<br />
|align="center"|[[File:Smyang.jpg|70px|link=people:SM_Yang]]<br />
|align="center"|[[File:배다솜.jpg|70px|link=People:DS Bae]]<br />
|align="center"|[[File:CY KIM.jpg|70px|link=People:CY_Kim]]<br />
|align="center"|[[File:Muyoung_Lee_2.jpg|70px|link=People:M_Lee]]<br />
|align="center"|[[File:Cho_JW.png|70px|link=People:J_Cho]]<br />
|align="center"|[[File:kim_EB.jpg|70px|link=People:E_Kim]]<br />
|-<br />
|align="center"|[[people:ER_Kim|Eiru Kim]]<br />
|align="center"|[[people:T_Lee|Tak Lee]]<br />
|align="center"|[[people:HJ_Han|Heon Jong Han]]<br />
|align="center"|[[people:KS_Kim|Kyungsoo Kim]]<br />
|align="center"|[[people:SM_Yang|Sunmo Yang]]<br />
|align="center"|[[People:DS Bae|Dasom Bae]]<br />
|align="center"|[[People:CY Kim|Chan Yeong Kim]]<br />
|align="center"|[[People:M_Lee|Muyoung Lee]]<br />
|align="center"|[[People:J_Cho|Jaewan Cho]]<br />
|align="center"|[[People:E_kim|Eunbeen Kim]]<br />
|-<br />
|align="center"|[[people:ER_Kim|PhD candidate]]<br />
|align="center"|[[people:T_Lee|PhD candidate]]<br />
|align="center"|[[People:HJ_Han|PhD course]]<br />
|align="center"|[[people:KS_Kim|PhD course]]<br />
|align="center"|[[people:SM_Yang|MS course/System Admin]]<br />
|align="center"|[[people:DS Bae|PhD course]]<br />
|align="center"|[[people:CY Kim|PhD course]]<br />
|align="center"|[[people:M_Lee|PhD course]]<br />
|align="center"|[[people:J_Cho|PhD course]]<br />
|align="center"|[[people:E_Kim|MS course]]<br />
|}<br />
<br />
=='''Undergraduate Students'''==<br />
<br />
<br />
=='''Visiting scientists/students'''==<br />
<br />
<br />
=='''Alumni'''==<br />
*Former Post-docs and Staff Scientists<br />
**Taeyun Oh (2009.5-2011.12), current position: Deputy Principal Consultant, INSILICOGEN (www.insilicogen.com) <br />
**Samuel Beck (2011.2-2011.12), current position; Postdoc fellow, University of Texas at Austin (Jonghwan Kim's Lab)<br />
**Jawon Song (2011.1-2012.5), current position; Research Scientist, Texas Advanced Computing Center, Austin, TX, USA<br />
**Yoonhee Ko (2012.8-2014.2), current position; Fellow, Severance Medical center (Yonsei Medical school)<br />
**Jonghoon Lee (2013.10-2014.2), current position; Assistant Professor, CHA Medical school <br />
**Sohyun Hwang (2010.3-2015.8), current position; Research Professor, Ewha Womans University<br />
<br />
*Former Graduate Students<br />
**Sungou Ji (2009.9-2011.8), MS; current position; Postdoc fellow, Sanger Genome Institute, Cambridge University, UK (Research field: Statistical Genomics)<br />
**Junha Shin (2008.9-2014.2), PhD; <br />
**Hanhae Kim (2008.9-2015.2), PhD; current position; Associate Research Fellow, Korea Institute of S&T Evaluation and Planning (KISTEP)<br />
**Ara Cho (2008.9-2015.2), PhD; <br />
**Hyojin Kim (2013.3-2015.2), MS; current position; Research Assistant, Samsung Advanced Institute for Health Sciences & Technology (SAIHST)<br />
**Hongseok Shim (2013.9-2015.8), MS; <br />
<br />
*Former Visiting Scientists/Students<br />
**Minkyung Shin (2012.3-2012.7), went to a graduate school, University of Southern California, USA<br />
**Paul Chung (2012 summer high school student intern), went to University of Pennsylvania (Bio Engineering) <br />
**Susie Shin (2013 summer high school student intern), went to Vanderbilt University (Bio Engineering)<br />
**Hyunjin Cho (Johns Hopkins University, Bioinformatics)<br />
<br />
*Former Undergraduate Students<br />
**Ila Shin, went to a medical school (Yonsei Univ.)<br />
**Yoonkyung Ko<br />
**Sangyo Park, went to a law school (Kyounghee Univ.)<br />
**Jayoon Shin, went to a medical school (Pusan National Univ.)<br />
**Dongjoo Sun, went to a dental school (Wongwang Univ.)<br />
**Eulsoo Kim<br />
**Myungwhan Lee, went to a medical school (Yonsei Univ.)<br />
**Moonhee Lee, went to a graduate school, University of Amsterdam, Netherlands<br />
**Jinhyun Ju, went to a graduate school, Cornell Medical School, NY, USA (Research field: Computational Systems Biology)<br />
**Haeyoung Shin, went to a graduate school, Brown University, USA (Research field: Computational Neuroscience)<br />
**Joonghee Soh, went to a graduate school, KAIST, Korea (Research field: Culture Technology)<br />
**Hee Jung Cho, went to a graduate school, UC Berkeley <br />
**TaeHwan Kim, went to a medical school<br />
**Joohyung Kim, went to a medical school (Kyungpook National Univ.)<br />
**Donghyun Shin, went to a medical school (Yonsei Univ.)<br />
**Sunphil Kim<br />
**Jaeho Shim<br />
**Seunghyun Shin</div>
Ds628
https://netbiolab.org/wiki/index.php?title=File:Cho_JW.png&diff=3858
File:Cho JW.png
2016-06-08T06:24:26Z
<p>Ds628: </p>
<hr />
<div></div>
Ds628
https://netbiolab.org/wiki/index.php?title=People&diff=3857
People
2016-06-08T06:23:17Z
<p>Ds628: /* Graduate Students */</p>
<hr />
<div>__NOTOC__<br />
=='''Principal Investigator'''==<br />
{|border="0" width="150"<br />
|align="center"|[[File:People_ISLee_03.jpg|77px|link=people:IS_Lee]]<br />
|-<br />
|align="center"|[[people:IS_Lee|Insuk Lee]]<br />
|-<br />
|}<br />
<br />
=='''Research Professor/Postdoc Fellow/Staff Scientist'''==<br />
{|border="0" width="300"<br />
|align="center"|[[File:People_JE_Shim_EDIT.JPG|70px|link=people:JE_Shim]]<br />
|align="center"|[[File:SYLee.jpg|70px|link=people:SY_Lee]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Jung Eun Shim]]<br />
|align="center"|[[people:SY_Lee|Sangyoung Lee]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Research Professor]]<br />
|align="center"|[[people:SY_Lee|Research Assistant]]<br />
|}<br />
<br />
=='''Graduate Students'''==<br />
{|border="0" width="900"<br />
|align="center" |[[File:Banmyungham.JPG|70px|link=people:ER_Kim]]<br />
|align="center" |[[File:Tak_sajin3.jpg|70px|link=people:T_Lee]]<br />
|align="center" |[[File:heonjong.jpg|70px|link=people:HJ_Han]]<br />
|align="center" |[[File:People_KSKim.jpg|70px|link=people:KS_Kim]]<br />
|align="center"|[[File:Smyang.jpg|70px|link=people:SM_Yang]]<br />
|align="center"|[[File:배다솜.jpg|70px|link=People:DS Bae]]<br />
|align="center"|[[File:CY KIM.jpg|70px|link=People:CY_Kim]]<br />
|align="center"|[[File:Muyoung_Lee_2.jpg|70px|link=People:M_Lee]]<br />
|align="center"|[[File:kim_EB.jpg|70px|link=People:E_Kim]]<br />
|-<br />
|align="center"|[[people:ER_Kim|Eiru Kim]]<br />
|align="center"|[[people:T_Lee|Tak Lee]]<br />
|align="center"|[[people:HJ_Han|Heon Jong Han]]<br />
|align="center"|[[people:KS_Kim|Kyungsoo Kim]]<br />
|align="center"|[[people:SM_Yang|Sunmo Yang]]<br />
|align="center"|[[People:DS Bae|Dasom Bae]]<br />
|align="center"|[[People:CY Kim|Chan Yeong Kim]]<br />
|align="center"|[[People:M_Lee|Muyoung Lee]]<br />
|align="center"|[[People:E_kim|Eunbeen Kim]]<br />
|-<br />
|align="center"|[[people:ER_Kim|PhD candidate]]<br />
|align="center"|[[people:T_Lee|PhD candidate]]<br />
|align="center"|[[People:HJ_Han|PhD course]]<br />
|align="center"|[[people:KS_Kim|PhD course]]<br />
|align="center"|[[people:SM_Yang|MS course/System Admin]]<br />
|align="center"|[[people:DS Bae|PhD course]]<br />
|align="center"|[[people:CY Kim|PhD course]]<br />
|align="center"|[[people:M_Lee|PhD course]]<br />
|align="center"|[[people:E_Kim|MS course]]<br />
|}<br />
<br />
=='''Undergraduate Students'''==<br />
<br />
<br />
=='''Visiting scientists/students'''==<br />
<br />
<br />
=='''Alumni'''==<br />
*Former Post-docs and Staff Scientists<br />
**Taeyun Oh (2009.5-2011.12), current position: Deputy Principal Consultant, INSILICOGEN (www.insilicogen.com) <br />
**Samuel Beck (2011.2-2011.12), current position; Postdoc fellow, University of Texas at Austin (Jonghwan Kim's Lab)<br />
**Jawon Song (2011.1-2012.5), current position; Research Scientist, Texas Advanced Computing Center, Austin, TX, USA<br />
**Yoonhee Ko (2012.8-2014.2), current position; Fellow, Severance Medical center (Yonsei Medical school)<br />
**Jonghoon Lee (2013.10-2014.2), current position; Assistant Professor, CHA Medical school <br />
**Sohyun Hwang (2010.3-2015.8), current position; Research Professor, Ewha Womans University<br />
<br />
*Former Graduate Students<br />
**Sungou Ji (2009.9-2011.8), MS; current position; Postdoc fellow, Sanger Genome Institute, Cambridge University, UK (Research field: Statistical Genomics)<br />
**Junha Shin (2008.9-2014.2), PhD; <br />
**Hanhae Kim (2008.9-2015.2), PhD; current position; Associate Research Fellow, Korea Institute of S&T Evaluation and Planning (KISTEP)<br />
**Ara Cho (2008.9-2015.2), PhD; <br />
**Hyojin Kim (2013.3-2015.2), MS; current position; Research Assistant, Samsung Advanced Institute for Health Sciences & Technology (SAIHST)<br />
**Hongseok Shim (2013.9-2015.8), MS; <br />
<br />
*Former Visiting Scientists/Students<br />
**Minkyung Shin (2012.3-2012.7), went to a graduate school, University of Southern California, USA<br />
**Paul Chung (2012 summer high school student intern), went to University of Pennsylvania (Bio Engineering) <br />
**Susie Shin (2013 summer high school student intern), went to Vanderbilt University (Bio Engineering)<br />
**Hyunjin Cho (Johns Hopkins University, Bioinformatics)<br />
<br />
*Former Undergraduate Students<br />
**Ila Shin, went to a medical school (Yonsei Univ.)<br />
**Yoonkyung Ko<br />
**Sangyo Park, went to a law school (Kyounghee Univ.)<br />
**Jayoon Shin, went to a medical school (Pusan National Univ.)<br />
**Dongjoo Sun, went to a dental school (Wongwang Univ.)<br />
**Eulsoo Kim<br />
**Myungwhan Lee, went to a medical school (Yonsei Univ.)<br />
**Moonhee Lee, went to a graduate school, University of Amsterdam, Netherlands<br />
**Jinhyun Ju, went to a graduate school, Cornell Medical School, NY, USA (Research field: Computational Systems Biology)<br />
**Haeyoung Shin, went to a graduate school, Brown University, USA (Research field: Computational Neuroscience)<br />
**Joonghee Soh, went to a graduate school, KAIST, Korea (Research field: Culture Technology)<br />
**Hee Jung Cho, went to a graduate school, UC Berkeley <br />
**TaeHwan Kim, went to a medical school<br />
**Joohyung Kim, went to a medical school (Kyungpook National Univ.)<br />
**Donghyun Shin, went to a medical school (Yonsei Univ.)<br />
**Sunphil Kim<br />
**Jaeho Shim<br />
**Seunghyun Shin</div>
Ds628
https://netbiolab.org/wiki/index.php?title=File:Kim_EB.jpg&diff=3856
File:Kim EB.jpg
2016-06-08T06:20:19Z
<p>Ds628: </p>
<hr />
<div></div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:Album:2015_Teachers%27_day&diff=3855
People:Album:2015 Teachers' day
2016-06-08T05:31:02Z
<p>Ds628: Undo revision 3848 by Ds628 (talk)</p>
<hr />
<div><gallery><br />
File:2015teachersday1.jpg<br />
File:2015teachersday2.jpg<br />
File:2015teachersday3.jpg<br />
</gallery></div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:Album:2016_Teachers%27_day&diff=3854
People:Album:2016 Teachers' day
2016-06-08T05:28:35Z
<p>Ds628: Created page with "<gallery> File:2016스승의날2.jpg File:2016스승의날1.jpg </gallery>"</p>
<hr />
<div><gallery><br />
File:2016스승의날2.jpg<br />
File:2016스승의날1.jpg<br />
</gallery></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Album&diff=3853
Album
2016-06-08T05:27:41Z
<p>Ds628: </p>
<hr />
<div>__NOTOC__<br />
=='''Group Photo'''==<br />
{|border="0" width="500"<br />
|<br />
[[File:P4070576 1.jpg|thumb|2016]]<br />
|align="center"|<br />
[[File:Groupphoto 20150601 2.jpeg|thumb|2015]]<br />
|align="center"|<br />
[[File:2014group3.JPG|thumb|2014]]<br />
|align="center"|<br />
[[File:2013단체1.jpg|thumb|2013]]<br />
|-<br />
|<br />
[[File:People_Album_Spring2012_main.jpg|thumb|2012]]<br />
|align="center"|<br />
[[File:People_Album_Spring2011_05.jpg|thumb|2011]]<br />
|align="center"|<br />
[[File:People_Album_Spring2010_01.jpg|thumb|2010]]<br />
|}<br />
----<br />
*[[People:Album:2016 Teachers' day | 2016 Teacher's day]]<br />
----<br />
*[[People:Album:2016 Group photo | 2016 Group photo]]<br />
----<br />
*[[People:Album:2015 Group photo | 2015 Group photo]]<br />
----<br />
*[[People:Album:2015 Teachers' day | 2015 Teacher's day]]<br />
----<br />
*[[People:Album:2014 Summer MT | 2014 Summer MT]]<br />
----<br />
*[[People:Album:2014 Group photo | 2014 Group photo]]<br />
----<br />
*[[People:Album:2013 Summer MT | 2013 Summer MT]]<br />
----<br />
*[[People:Album:2013 Group photo | 2013 Group photo]]<br />
----<br />
*[[People:Album:Teachers' day 2013| 2013 May, Teachers' day]]<br />
----<br />
*[[People:Album:ThanksGivingDay_2012| 2012 Nov, Thanksgiving Day]]<br />
----<br />
*[[People:Album:MT_2012| 2012 June, Summer MT]]<br />
----<br />
*[[People:Album:GroupPhoto_2012_Spring|2012 April, Group Photo]]<br />
----<br />
*[[People:Album:Keystone_2012| 2012 February, Keystone]]<br />
----<br />
*[[People:Album:MT_2011| 2011 August, Summer MT]]<br />
----<br />
*[[People:Album:ISSCR_2011| 2011 June, ISSCR]]<br />
----<br />
*[[People:Album:RECOMB_2011| 2011 March, RECOMB2011]]<br />
----<br />
*[[People:Album:AYRCOB5th_2011| 2011 August, Ayrcob 5th]]<br />
----<br />
*[[People:Album:Teachers_Day_2011| 2011 May, Teacher's day]]<br />
----<br />
*[[People:Album:GroupPhoto_2011_Spring|2011 March, Group Photo]]<br />
----<br />
*[[People:Album:APBC2011|2011 February, APBC (Incheon)]]<br />
----<br />
*[[People:Album:ISMB2010|2010 June, ISMB(Boston)]]<br />
----<br />
*[[People:Album:Sue2010|2010 June, Sue Rhee visit]]<br />
----<br />
*[[People:Album:Cup_cake_2010| 2010 May, Cup Cake professor]]<br />
----<br />
*[[People:Album:Edward_Marcotte_at_NBL|2010 May, Edward Marcotte and @NBL Reunion]]<br />
----<br />
*[[People:Album:GroupPhoto_2010_Spring|2010 March, Group Photo]]<br />
----<br />
*[[People:Album:KSBSB2009|2009 November, KSBSB (Pusan)]]<br />
----<br />
*[[People:Album:ICSB2009|2009 August, ICSB (Stanford)]]<br />
----<br />
*[[People:Album:winter_MT_2008|2008 December, Winter MT]]</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:CY_Kim&diff=3852
People:CY Kim
2016-06-08T05:24:36Z
<p>Ds628: /* Chan Young Kim */</p>
<hr />
<div>===Chan Young Kim===<br />
{|<br />
|[[File:CY KIM.jpg|300px]]<br />
|'''Ph.D program student'''(2015~) Department of Biotechnology, Yonsei University<br />
(2010-2014) Department of Biotechnology, Yonsei University<br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:M_Lee&diff=3851
People:M Lee
2016-06-08T05:24:07Z
<p>Ds628: /* Muyoung Lee */</p>
<hr />
<div>===Muyoung Lee===<br />
{|<br />
|[[File:Muyoung_Lee_2.jpg|300px]]<br />
|'''Ph.D program student'''(2016~) Department of Biotechnology, Yonsei University<br />
(2010-2015) Department of biochemistry, Yonsei University<br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:CY_Kim&diff=3850
People:CY Kim
2016-06-08T05:21:15Z
<p>Ds628: /* Chan Young Kim */</p>
<hr />
<div>===Chan Young Kim===<br />
{|<br />
|[[File:CY KIM.jpg|300px]]<br />
|'''Ph.D program student'''(2015~) Department of Biotechnology, Yonsei University<br />
(2010-2015) Department of Biotechnology, Yonsei University<br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:CY_Kim&diff=3849
People:CY Kim
2016-06-08T05:20:22Z
<p>Ds628: /* Chan Young Kim */</p>
<hr />
<div>===Chan Young Kim===<br />
{|<br />
|[[File:CY KIM.jpg|300px]]<br />
|(2010-2015) Department of Biotechnology, Yonsei University<br />
|(2015~) Department of Biotechnology, Yonsei University<br />
|}</div>
Ds628
https://netbiolab.org/wiki/index.php?title=People:Album:2015_Teachers%27_day&diff=3848
People:Album:2015 Teachers' day
2016-06-08T05:17:29Z
<p>Ds628: </p>
<hr />
<div><gallery><br />
File:2016스승의날2.jpg<br />
File:2016스승의날1.jpg<br />
</gallery></div>
Ds628
https://netbiolab.org/wiki/index.php?title=File:2016%EC%8A%A4%EC%8A%B9%EC%9D%98%EB%82%A02.jpg&diff=3847
File:2016스승의날2.jpg
2016-06-08T05:16:34Z
<p>Ds628: </p>
<hr />
<div></div>
Ds628
https://netbiolab.org/wiki/index.php?title=File:2016%EC%8A%A4%EC%8A%B9%EC%9D%98%EB%82%A01.jpg&diff=3846
File:2016스승의날1.jpg
2016-06-08T05:16:18Z
<p>Ds628: </p>
<hr />
<div></div>
Ds628
https://netbiolab.org/wiki/index.php?title=Album&diff=3845
Album
2016-06-08T05:15:14Z
<p>Ds628: /* Group Photo */</p>
<hr />
<div>__NOTOC__<br />
=='''Group Photo'''==<br />
{|border="0" width="500"<br />
|<br />
[[File:P4070576 1.jpg|thumb|2016]]<br />
|align="center"|<br />
[[File:Groupphoto 20150601 2.jpeg|thumb|2015]]<br />
|align="center"|<br />
[[File:2014group3.JPG|thumb|2014]]<br />
|align="center"|<br />
[[File:2013단체1.jpg|thumb|2013]]<br />
|-<br />
|<br />
[[File:People_Album_Spring2012_main.jpg|thumb|2012]]<br />
|align="center"|<br />
[[File:People_Album_Spring2011_05.jpg|thumb|2011]]<br />
|align="center"|<br />
[[File:People_Album_Spring2010_01.jpg|thumb|2010]]<br />
|}<br />
----<br />
*[[People:Album:2015 Teachers' day | 2016 Teacher's day]]<br />
----<br />
*[[People:Album:2016 Group photo | 2016 Group photo]]<br />
----<br />
*[[People:Album:2015 Group photo | 2015 Group photo]]<br />
----<br />
*[[People:Album:2015 Teachers' day | 2015 Teacher's day]]<br />
----<br />
*[[People:Album:2014 Summer MT | 2014 Summer MT]]<br />
----<br />
*[[People:Album:2014 Group photo | 2014 Group photo]]<br />
----<br />
*[[People:Album:2013 Summer MT | 2013 Summer MT]]<br />
----<br />
*[[People:Album:2013 Group photo | 2013 Group photo]]<br />
----<br />
*[[People:Album:Teachers' day 2013| 2013 May, Teachers' day]]<br />
----<br />
*[[People:Album:ThanksGivingDay_2012| 2012 Nov, Thanksgiving Day]]<br />
----<br />
*[[People:Album:MT_2012| 2012 June, Summer MT]]<br />
----<br />
*[[People:Album:GroupPhoto_2012_Spring|2012 April, Group Photo]]<br />
----<br />
*[[People:Album:Keystone_2012| 2012 February, Keystone]]<br />
----<br />
*[[People:Album:MT_2011| 2011 August, Summer MT]]<br />
----<br />
*[[People:Album:ISSCR_2011| 2011 June, ISSCR]]<br />
----<br />
*[[People:Album:RECOMB_2011| 2011 March, RECOMB2011]]<br />
----<br />
*[[People:Album:AYRCOB5th_2011| 2011 August, Ayrcob 5th]]<br />
----<br />
*[[People:Album:Teachers_Day_2011| 2011 May, Teacher's day]]<br />
----<br />
*[[People:Album:GroupPhoto_2011_Spring|2011 March, Group Photo]]<br />
----<br />
*[[People:Album:APBC2011|2011 February, APBC (Incheon)]]<br />
----<br />
*[[People:Album:ISMB2010|2010 June, ISMB(Boston)]]<br />
----<br />
*[[People:Album:Sue2010|2010 June, Sue Rhee visit]]<br />
----<br />
*[[People:Album:Cup_cake_2010| 2010 May, Cup Cake professor]]<br />
----<br />
*[[People:Album:Edward_Marcotte_at_NBL|2010 May, Edward Marcotte and @NBL Reunion]]<br />
----<br />
*[[People:Album:GroupPhoto_2010_Spring|2010 March, Group Photo]]<br />
----<br />
*[[People:Album:KSBSB2009|2009 November, KSBSB (Pusan)]]<br />
----<br />
*[[People:Album:ICSB2009|2009 August, ICSB (Stanford)]]<br />
----<br />
*[[People:Album:winter_MT_2008|2008 December, Winter MT]]</div>
Ds628
https://netbiolab.org/wiki/index.php?title=Album&diff=3844
Album
2016-06-08T05:14:44Z
<p>Ds628: /* Group Photo */</p>
<hr />
<div>__NOTOC__<br />
=='''Group Photo'''==<br />
{|border="0" width="500"<br />
|<br />
[[File:P4070576 1.jpg|thumb|2016]]<br />
|align="center"|<br />
[[File:Groupphoto 20150601 2.jpeg|thumb|2015]]<br />
|align="center"|<br />
[[File:2014group3.JPG|thumb|2014]]<br />
|align="center"|<br />
[[File:2013단체1.jpg|thumb|2013]]<br />
|-<br />
|<br />
[[File:People_Album_Spring2012_main.jpg|thumb|2012]]<br />
|align="center"|<br />
[[File:People_Album_Spring2011_05.jpg|thumb|2011]]<br />
|align="center"|<br />
[[File:People_Album_Spring2010_01.jpg|thumb|2010]]<br />
|}<br />
----<br />
*[[People:Album:2015 Teachers' day | 2015 Teacher's day]]<br />
----<br />
*[[People:Album:2016 Group photo | 2016 Group photo]]<br />
----<br />
*[[People:Album:2015 Group photo | 2015 Group photo]]<br />
----<br />
*[[People:Album:2015 Teachers' day | 2015 Teacher's day]]<br />
----<br />
*[[People:Album:2014 Summer MT | 2014 Summer MT]]<br />
----<br />
*[[People:Album:2014 Group photo | 2014 Group photo]]<br />
----<br />
*[[People:Album:2013 Summer MT | 2013 Summer MT]]<br />
----<br />
*[[People:Album:2013 Group photo | 2013 Group photo]]<br />
----<br />
*[[People:Album:Teachers' day 2013| 2013 May, Teachers' day]]<br />
----<br />
*[[People:Album:ThanksGivingDay_2012| 2012 Nov, Thanksgiving Day]]<br />
----<br />
*[[People:Album:MT_2012| 2012 June, Summer MT]]<br />
----<br />
*[[People:Album:GroupPhoto_2012_Spring|2012 April, Group Photo]]<br />
----<br />
*[[People:Album:Keystone_2012| 2012 February, Keystone]]<br />
----<br />
*[[People:Album:MT_2011| 2011 August, Summer MT]]<br />
----<br />
*[[People:Album:ISSCR_2011| 2011 June, ISSCR]]<br />
----<br />
*[[People:Album:RECOMB_2011| 2011 March, RECOMB2011]]<br />
----<br />
*[[People:Album:AYRCOB5th_2011| 2011 August, Ayrcob 5th]]<br />
----<br />
*[[People:Album:Teachers_Day_2011| 2011 May, Teacher's day]]<br />
----<br />
*[[People:Album:GroupPhoto_2011_Spring|2011 March, Group Photo]]<br />
----<br />
*[[People:Album:APBC2011|2011 February, APBC (Incheon)]]<br />
----<br />
*[[People:Album:ISMB2010|2010 June, ISMB(Boston)]]<br />
----<br />
*[[People:Album:Sue2010|2010 June, Sue Rhee visit]]<br />
----<br />
*[[People:Album:Cup_cake_2010| 2010 May, Cup Cake professor]]<br />
----<br />
*[[People:Album:Edward_Marcotte_at_NBL|2010 May, Edward Marcotte and @NBL Reunion]]<br />
----<br />
*[[People:Album:GroupPhoto_2010_Spring|2010 March, Group Photo]]<br />
----<br />
*[[People:Album:KSBSB2009|2009 November, KSBSB (Pusan)]]<br />
----<br />
*[[People:Album:ICSB2009|2009 August, ICSB (Stanford)]]<br />
----<br />
*[[People:Album:winter_MT_2008|2008 December, Winter MT]]</div>
Ds628