Difference between revisions of "Journal Club"

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|Paper_index
 
|Paper_index
 
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{| border ="1"
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|rowspan = "3" |
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|rowspan = "3" |March 5 Mon, 2012
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|rowspan = "3" |
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|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]
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|-
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|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]
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|-
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|[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 ]
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|-
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|rowspan = "7" |***
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|rowspan = "7" |February 27 Mon~28 Tue, 2012
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|rowspan = "7" |
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|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]
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|-
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|[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]
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|-
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|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]
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|-
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|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]
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|-
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|[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]
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|-
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|[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]
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|-
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|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]
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|-
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|rowspan = "5" |
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|rowspan = "5" |February 6 Mon, 2012
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|rowspan = "5" |
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|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]
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|-
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|[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]
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|-
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|[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]
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|-
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|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]
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|-
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|[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]
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|-
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|rowspan = "5" |
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|rowspan = "5" |January 30 Mon, 2012
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|rowspan = "5" |
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|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]
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|-
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|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]
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|-
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|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]
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|-
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|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]
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|-
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|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]
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|-
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|rowspan = "3" |
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|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012
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|rowspan = "3" |
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|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]
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|-
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|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]
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|-
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|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]
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|-
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|rowspan = "6" |
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|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012
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|rowspan = "6" |
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|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]
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|-
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|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]
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|-
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|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]
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|-
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|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]
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|-
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|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]
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|-
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|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]
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|-
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|rowspan = "3" |
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|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012
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|rowspan = "3" |
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|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]
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|-
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|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]
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|-
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|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]
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|-
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|rowspan = "2" |
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|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012
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|rowspan = "2" |
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|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]
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|-
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|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]
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|-
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|rowspan = "6" |
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|rowspan = "6" |November 28 Mon, 2011
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|rowspan = "6" | TY Oh, <br>
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SH Hwang, <br>
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JE Shim, <br>
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S Beck, <br>
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JH Shin
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|[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]
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|-
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|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]
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|-
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|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]
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|-
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|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]
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|-
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|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]
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|-
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|[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]
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|-
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|rowspan = "3" |
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|rowspan = "3" |November 14 Mon, 2011
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|rowspan = "3" | HH Kim & AR Cho
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|[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]
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|-
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|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]
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|-
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|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]
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|-
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|rowspan = "4" |
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|rowspan = "4" |November 7 Mon, 2011
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|rowspan = "4" | YH Ko
 +
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]
 +
|-
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|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]
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|-
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|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]
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|-
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|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]
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|-
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|rowspan = "3" |
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|rowspan = "3" |November 7 Mon, 2011
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|rowspan = "3" | JW Song
 +
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]
 +
|-
 +
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]
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|-
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|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]
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|-
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|rowspan = "3" |
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|rowspan = "3" |October 5 Mon, 2011
 +
|rowspan = "3" | HH Kim
 +
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]
 +
|-
 +
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]
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|-
 +
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]
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|-
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|rowspan = "4" |
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|rowspan = "4" |October 4 Mon, 2011
 +
|rowspan = "4" | S Beck
 +
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]
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|-
 +
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html  Molecular eco-systems biology: towards an understanding of community function]
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|-
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|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]
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|-
 +
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]
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|-
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|rowspan = "2" |
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|rowspan = "2" |September 19 Mon, 2011
 +
|rowspan = "2" | TY Oh
 +
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]
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|-
 +
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]
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|-
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|rowspan = "2" |
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|rowspan = "2" |September 5 Mon, 2011
 +
|SG Ji
 +
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]
 +
|-
 +
|SH Hwang
 +
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]
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|-
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|rowspan = "2" |
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|rowspan = "2" | August 22 Mon, 2011
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|ER Kim
 +
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]
 +
|-
 +
|T Lee
 +
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]
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|-
 +
|
 +
|June 20 Mon, 2011
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|JH Shin
 +
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]
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|-
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|rowspan = "2" |
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|rowspan = "2" | May 30 Mon, 2011
 +
|rowspan = "2" | HH Kim
 +
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]
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|-
 +
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]
 
|-
 
|-
 +
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|rowspan = "2" |
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|rowspan = "2" | May 16 Mon, 2011
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|rowspan = "2" | AR Cho
 +
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']
 +
|-
 +
|[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]
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|-
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|rowspan = "3" |
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|rowspan = "3" |April 25 Mon, 2011
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|rowspan = "3" |S Beck
 +
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]
 +
|-
 +
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]
 +
|-
 +
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]
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|-
 +
|rowspan = "2" |
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|rowspan = "2" |April 11 Mon, 2011
 +
|JE Shim
 +
|[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]
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|-
 +
|T Lee
 +
|***Changed!***
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[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]
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|-
 +
|rowspan = "2"|
 +
|rowspan = "2"|March 28 Mon, 2011
 +
|rowspan = "2"|TY Oh
 +
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]
 +
|-
 +
|[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]
 +
|-
 +
|rowspan = "2"|
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|rowspan = "2"|March 14 Mon, 2011
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|rowspan = "2"|JW Song
 +
|[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]
 +
|-
 +
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]
 +
|-
 +
 +
|rowspan = "2"|
 +
|rowspan = "2"|February 28 Mon, 2011
 +
|KS Kim
 +
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]
 +
|-
 +
|HJ Han
 +
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]
 +
|-
 +
|
 +
|February 21 Mon, 2011
 +
|MH Lee
 +
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]
 +
|-
 +
|
 +
|February 14 Mon, 2011
 +
|AR Cho
 +
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]
 +
|-
 +
|rowspan = "2"|
 +
|rowspan = "2"|January 31 Mon, 2011
 +
|rowspan = "2"|JW Song
 +
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]
 +
|-
 +
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]
 +
|-
 +
|rowspan = "2"|
 +
|rowspan = "2" | December 27 Mon, 2010
 +
|ER Kim
 +
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]
 +
|-
 +
|T Lee
 +
|[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]
 +
|-
 +
|rowspan = "2"|
 +
|rowspan = "2"|November 15 Mon, 2010
 +
|AR Cho
 +
|[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]
 +
|-
 +
|SG Ji
 +
|[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]
 +
|-
 +
|rowspan = "2"|
 +
|rowspan = "2"|November 1 Mon, 2010
 +
|HH Kim
 +
|[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]
 +
|-
 +
|JH Shin
 +
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]
 +
|-
 +
|
 +
|October 11 Mon, 2010
 +
|JE Shim
 +
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]
 +
|-
 +
|
 +
|September 13 Mon, 2010
 +
|SH Hwang
 +
|[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]
 +
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]
 +
|-
 +
|
 +
|May 26 Wed, 2010
 +
|AR Cho
 +
|[[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]]
 +
|-
 +
|
 +
|May 19 Wed, 2010
 +
|SG Ji
 +
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]
 +
|-
 +
|
 +
|April 21 Wed, 2010
 +
|JH Shin
 +
|[[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]]
 +
|-
 +
|
 +
|April 14 Wed, 2010
 +
|TY Oh
 +
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]
 +
|-
 +
|rowspan = "2" |
 +
|rowspan = "2" |April 7 Wed, 2010
 +
|HHkim
 +
|
 +
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]
 +
|-
 +
|T Lee
 +
|
 +
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]
 +
|-
 +
|
 +
|Mar 31 Wed, 2010
 +
|JE Shim
 +
|[[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]]
 +
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]
 +
|-
 +
|
 +
|Mar 24 Wed, 2010
 +
|SH Hwang
 +
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]
 +
|-
 +
|
 +
|Jan 18 Mon, 2010
 +
|TY Oh(T Lee)
 +
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies
 +
|-
 +
|
 +
|Jan 16 Sat, 2010
 +
|JE Shim(MH Lee)
 +
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells
 +
|-
 +
|
 +
|Jan 15 Fri, 2010
 +
|SG Ji
 +
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions
 +
|-
 +
|
 +
|Jan 14 Thu, 2010
 +
|HH kim
 +
|chemogenomic_profiling_predicts_antifungal_synergies
 +
|-
 +
|
 +
|Jan 13 Wed, 2010
 +
|JH Shin(ER Kim)
 +
|edgetic_perturbation_models_of_human_inherited_disorders
 +
|-
 +
|
 +
|Jan 12 Tue, 2010
 +
|TY Oh(T Lee)
 +
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans
 +
|-
 +
|
 +
|Jan 11 Mon, 2010
 +
|JE Shim(MH Lee)
 +
|predicting_new_molecular_targets_for_known_drugs.pdf
 +
Reference:SEA(Similarity Ensemble Approach)
 +
|-
 +
|
 +
|Jan 09 Sat, 2010
 +
|SG Ji
 +
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance
 +
|-
 +
|
 +
|Jan 08 Fri, 2010
 +
|AR Cho
 +
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer
 +
|-
 +
|
 +
|Jan 07 Thu, 2010
 +
|HH Kim
 +
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network
 +
|-
 +
|
 +
|Jan 06 Wed, 2010
 +
|JH Shin(ER Kim)
 +
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs
 +
|}
  
 
|}
 
|}

Revision as of 13:34, 4 March 2012

Date Paper_index Paper_title
March 5 Mon, 2012 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.
(11,Go&Ju)Differential expression analysis for sequence count data
(12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
*** February 27 Mon~28 Tue, 2012 (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics
(2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq
(3,HJ Han)From RNA-seq reads to differential expression results
(4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods
(5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq
(6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
(7,So&Shin)TopHat: discovering splice junctions with RNA-Seq
February 6 Mon, 2012 mirConnX: condition-specific mRNA-microRNA network integrator
Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data
A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures
Reprogramming of miRNA networks in cancer and leukemia
An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma
January 30 Mon, 2012 Principles and Strategies for Developing Network Models in Cancer
Reverse engineering of regulatory networks in human B cells
Variations in DNA elucidate molecular networks that cause disease
Harnessing gene expression to identify the genetic basis of drug resistance
An Integrated Approach to Uncover Drivers of Cancer
January 9 Mon, 2012
January 16 Mon, 2012 		Genetic variation in an individual human exome.
Predicting phenotypic variation in yeast from individual genome sequences.
Clinical assessment incorporating a personal genome.
January 9 Mon, 2012
January 16 Mon, 2012 		Human allelic variation: perspective from protein function, structure, and evolution.
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.
Prediction of deleterious human alleles.
Human non-synonymous SNPs: server and survey.
A method and server for predicting damaging missense mutations.
SNAP: predict effect of non-synonymous polymorphisms on function
January 9 Mon, 2012
January 16 Mon, 2012 		Computational and statistical approaches to analyzing variants identified by exome sequencing.
Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.
Targeted capture and massively parallel sequencing of 12 human exomes.
January 9 Mon, 2012
January 16 Mon, 2012 		The distribution of fitness effects of new mutations.
Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies
November 28 Mon, 2011 TY Oh,

SH Hwang,
JE Shim,
S Beck,
JH Shin

(Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events
(Shin)Network pharmacology: the next paradigm in drug discovery
(Oh)Systematic exploration of synergistic drug pairs
(Shim)Chemogenomic profiling predicts antifungal synergies
(Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery
(Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines
November 14 Mon, 2011 HH Kim & AR Cho Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets
Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole
Analysis of multiple compound–protein interactions reveals novel bioactive molecules
November 7 Mon, 2011 YH Ko Drug—target network
A side effect resource to capture phenotypic effects of drugs
Quantitative systems-level determinants of human genes targeted by successful drugs
Drug Target Identification Using Side-Effect Similarity
November 7 Mon, 2011 JW Song Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data
Exploiting drug–disease relationships for computational drug repositioning
Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks
October 5 Mon, 2011 HH Kim Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families
Quantifying environmental adaptation of metabolic pathways in metagenomics
Quantitative assessment of protein function prediction from metagenomics shotgun sequences
October 4 Mon, 2011 S Beck A human gut microbial gene catalogue established by metagenomic sequencing
Molecular eco-systems biology: towards an understanding of community function
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
Unravelling the effects of the environment and host genotype on the gut microbiome
September 19 Mon, 2011 TY Oh independently evolved virulence effectors converge onto hubs in a plant immune system Network
Evidence for network evolution in an arabidopsis interactome Map
September 5 Mon, 2011 SG Ji Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy
SH Hwang Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers
August 22 Mon, 2011 ER Kim Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks
T Lee From expression QTLs to personalized transcriptomics
June 20 Mon, 2011 JH Shin a user's guide to the encyclopedia of DNA elements(ENCODE)
May 30 Mon, 2011 HH Kim enterotypes of the human gut microbiome
toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data
May 16 Mon, 2011 AR Cho variable pathogenicity determines individual lifespan in caenorhabditis elegans
a high-resolution c.elegans essential gene network based on phenotypic profiling of a complex tissue
April 25 Mon, 2011 S Beck Hallmarks of Cancer : The next generation
Mapping Cancer Origins
Genetic Interactions in Cancer Progression and Treatment
April 11 Mon, 2011 JE Shim Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology
T Lee ***Changed!***

Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions

March 28 Mon, 2011 TY Oh profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis
cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control
March 14 Mon, 2011 JW Song phenotypic landscape of a bacterial cell
cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action
February 28 Mon, 2011 KS Kim genomic patterns of pleiotropy and the evolution of complexity
HJ Han simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway
February 21 Mon, 2011 MH Lee dynamic interaction networks in a hierarchically organized tissue
February 14 Mon, 2011 AR Cho rewiring of genetic networks in response to DNA damage
January 31 Mon, 2011 JW Song Applying mass spectrometry-based proteomics to genetics, genomics and network biology
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
December 27 Mon, 2010 ER Kim Functional_roles_fornoise_in_genetic_circuits
T Lee Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries
November 15 Mon, 2010 AR Cho Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes
SG Ji It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks
November 1 Mon, 2010 HH Kim A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes
JH Shin A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster
October 11 Mon, 2010 JE Shim Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders
September 13 Mon, 2010 SH Hwang Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells

Limits_of_sequence_and_functional_conservation

May 26 Wed, 2010 AR Cho network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf
May 19 Wed, 2010 SG Ji interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf
April 21 Wed, 2010 JH Shin identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf
April 14 Wed, 2010 TY Oh an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man
April 7 Wed, 2010 HHkim

systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes

T Lee

genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines

Mar 31 Wed, 2010 JE Shim toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf

systems_biology_of_stem_cell_fate_and_cellular_reprogramming

Mar 24 Wed, 2010 SH Hwang dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome
Jan 18 Mon, 2010 TY Oh(T Lee) JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies
Jan 16 Sat, 2010 JE Shim(MH Lee) systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells
Jan 15 Fri, 2010 SG Ji distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions
Jan 14 Thu, 2010 HH kim chemogenomic_profiling_predicts_antifungal_synergies
Jan 13 Wed, 2010 JH Shin(ER Kim) edgetic_perturbation_models_of_human_inherited_disorders
Jan 12 Tue, 2010 TY Oh(T Lee) analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans
Jan 11 Mon, 2010 JE Shim(MH Lee) predicting_new_molecular_targets_for_known_drugs.pdf

Reference:SEA(Similarity Ensemble Approach)

Jan 09 Sat, 2010 SG Ji harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance
Jan 08 Fri, 2010 AR Cho an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer
Jan 07 Thu, 2010 HH Kim a_phenotypic_profile_of_the_candida_albicans_regulatory_network
Jan 06 Wed, 2010 JH Shin(ER Kim) a_global_view_of_protein_expression_in_human_cells_tissues_and_organs


March 5 Mon, 2012 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.
(11,Go&Ju)Differential expression analysis for sequence count data
(12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
*** February 27 Mon~28 Tue, 2012 (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics
(2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq
(3,HJ Han)From RNA-seq reads to differential expression results
(4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods
(5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq
(6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
(7,So&Shin)TopHat: discovering splice junctions with RNA-Seq
February 6 Mon, 2012 mirConnX: condition-specific mRNA-microRNA network integrator
Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data
A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures
Reprogramming of miRNA networks in cancer and leukemia
An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma
January 30 Mon, 2012 Principles and Strategies for Developing Network Models in Cancer
Reverse engineering of regulatory networks in human B cells
Variations in DNA elucidate molecular networks that cause disease
Harnessing gene expression to identify the genetic basis of drug resistance
An Integrated Approach to Uncover Drivers of Cancer
January 9 Mon, 2012
January 16 Mon, 2012 		Genetic variation in an individual human exome.
Predicting phenotypic variation in yeast from individual genome sequences.
Clinical assessment incorporating a personal genome.
January 9 Mon, 2012
January 16 Mon, 2012 		Human allelic variation: perspective from protein function, structure, and evolution.
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.
Prediction of deleterious human alleles.
Human non-synonymous SNPs: server and survey.
A method and server for predicting damaging missense mutations.
SNAP: predict effect of non-synonymous polymorphisms on function
January 9 Mon, 2012
January 16 Mon, 2012 		Computational and statistical approaches to analyzing variants identified by exome sequencing.
Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.
Targeted capture and massively parallel sequencing of 12 human exomes.
January 9 Mon, 2012
January 16 Mon, 2012 		The distribution of fitness effects of new mutations.
Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies
November 28 Mon, 2011 TY Oh,

SH Hwang,
JE Shim,
S Beck,
JH Shin

(Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events
(Shin)Network pharmacology: the next paradigm in drug discovery
(Oh)Systematic exploration of synergistic drug pairs
(Shim)Chemogenomic profiling predicts antifungal synergies
(Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery
(Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines
November 14 Mon, 2011 HH Kim & AR Cho Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets
Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole
Analysis of multiple compound–protein interactions reveals novel bioactive molecules
November 7 Mon, 2011 YH Ko Drug—target network
A side effect resource to capture phenotypic effects of drugs
Quantitative systems-level determinants of human genes targeted by successful drugs
Drug Target Identification Using Side-Effect Similarity
November 7 Mon, 2011 JW Song Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data
Exploiting drug–disease relationships for computational drug repositioning
Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks
October 5 Mon, 2011 HH Kim Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families
Quantifying environmental adaptation of metabolic pathways in metagenomics
Quantitative assessment of protein function prediction from metagenomics shotgun sequences
October 4 Mon, 2011 S Beck A human gut microbial gene catalogue established by metagenomic sequencing
Molecular eco-systems biology: towards an understanding of community function
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
Unravelling the effects of the environment and host genotype on the gut microbiome
September 19 Mon, 2011 TY Oh independently evolved virulence effectors converge onto hubs in a plant immune system Network
Evidence for network evolution in an arabidopsis interactome Map
September 5 Mon, 2011 SG Ji Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy
SH Hwang Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers
August 22 Mon, 2011 ER Kim Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks
T Lee From expression QTLs to personalized transcriptomics
June 20 Mon, 2011 JH Shin a user's guide to the encyclopedia of DNA elements(ENCODE)
May 30 Mon, 2011 HH Kim enterotypes of the human gut microbiome
toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data
May 16 Mon, 2011 AR Cho variable pathogenicity determines individual lifespan in caenorhabditis elegans
a high-resolution c.elegans essential gene network based on phenotypic profiling of a complex tissue
April 25 Mon, 2011 S Beck Hallmarks of Cancer : The next generation
Mapping Cancer Origins
Genetic Interactions in Cancer Progression and Treatment
April 11 Mon, 2011 JE Shim Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology
T Lee ***Changed!***

Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions

March 28 Mon, 2011 TY Oh profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis
cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control
March 14 Mon, 2011 JW Song phenotypic landscape of a bacterial cell
cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action
February 28 Mon, 2011 KS Kim genomic patterns of pleiotropy and the evolution of complexity
HJ Han simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway
February 21 Mon, 2011 MH Lee dynamic interaction networks in a hierarchically organized tissue
February 14 Mon, 2011 AR Cho rewiring of genetic networks in response to DNA damage
January 31 Mon, 2011 JW Song Applying mass spectrometry-based proteomics to genetics, genomics and network biology
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
December 27 Mon, 2010 ER Kim Functional_roles_fornoise_in_genetic_circuits
T Lee Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries
November 15 Mon, 2010 AR Cho Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes
SG Ji It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks
November 1 Mon, 2010 HH Kim A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes
JH Shin A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster
October 11 Mon, 2010 JE Shim Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders
September 13 Mon, 2010 SH Hwang Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells

Limits_of_sequence_and_functional_conservation

May 26 Wed, 2010 AR Cho network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf
May 19 Wed, 2010 SG Ji interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf
April 21 Wed, 2010 JH Shin identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf
April 14 Wed, 2010 TY Oh an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man
April 7 Wed, 2010 HHkim

systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes

T Lee

genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines

Mar 31 Wed, 2010 JE Shim toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf

systems_biology_of_stem_cell_fate_and_cellular_reprogramming

Mar 24 Wed, 2010 SH Hwang dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome
Jan 18 Mon, 2010 TY Oh(T Lee) JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies
Jan 16 Sat, 2010 JE Shim(MH Lee) systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells
Jan 15 Fri, 2010 SG Ji distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions
Jan 14 Thu, 2010 HH kim chemogenomic_profiling_predicts_antifungal_synergies
Jan 13 Wed, 2010 JH Shin(ER Kim) edgetic_perturbation_models_of_human_inherited_disorders
Jan 12 Tue, 2010 TY Oh(T Lee) analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans
Jan 11 Mon, 2010 JE Shim(MH Lee) predicting_new_molecular_targets_for_known_drugs.pdf

Reference:SEA(Similarity Ensemble Approach)

Jan 09 Sat, 2010 SG Ji harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance
Jan 08 Fri, 2010 AR Cho an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer
Jan 07 Thu, 2010 HH Kim a_phenotypic_profile_of_the_candida_albicans_regulatory_network
Jan 06 Wed, 2010 JH Shin(ER Kim) a_global_view_of_protein_expression_in_human_cells_tissues_and_organs

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