Teaching

2019-03-26T08:07:07Z

Dreadcupper:

== Teaching materials for Experiment in microbiology and biochemical engineering laboratory Course ==
[//netbiolab.org/wiki/images/8/8e/2019_nbl_experiment.pdf 2019 netbiolab experiment teaching material]

[//netbiolab.org/wiki/images/8/8e/2019_수업자료.zip 2019 netbiolab experiment teaching material]

== Teaching materials for Yonsei Bioinformatics Course ==
[//netbiolab.org/wiki/Kallisto_materials.zip 2018 Bioinformatics Kallisto Practice]

[//netbiolab.org/wiki/WebMev_materials.zip 2018 Bioinformatics WebMeV Practice]

[//netbiolab.org/wiki/Bioinformatics_Machine_Learning_Practice.zip 2018 Bioinformatics Machine Learning Practice]

== Teaching materials for BIML workshop ==

[https://www.netbiolab.org/wiki/images/7/7b/2017_BIML_0216_2.zip BIML2017 practice 2 PPT file & python scripts]

[http://www.netbiolab.org/wiki/images/4/4b/Practice1.pdf BIML2016 practice 1 PPT file]

[http://www.netbiolab.org/wiki/images/c/c0/Biml_python_scripts.zip BIML2016 practice 2 python scripts]

<div>{{#widget:AddHtml|content=<img src="../wiki/wordcloud_2013_2017.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div>

Teaching

2019-03-26T08:06:42Z

Dreadcupper:

== Teaching materials for Experiment in microbiology and biochemical engineering laboratory Course ==
[//https://netbiolab.org/wiki/images/8/8e/2019_nbl_experiment.pdf 2019 netbiolab experiment teaching material]

[//https://netbiolab.org/wiki/images/8/8e/2019_수업자료.zip 2019 netbiolab experiment teaching material]

== Teaching materials for Yonsei Bioinformatics Course ==
[//netbiolab.org/wiki/Kallisto_materials.zip 2018 Bioinformatics Kallisto Practice]

[//netbiolab.org/wiki/WebMev_materials.zip 2018 Bioinformatics WebMeV Practice]

[//netbiolab.org/wiki/Bioinformatics_Machine_Learning_Practice.zip 2018 Bioinformatics Machine Learning Practice]

== Teaching materials for BIML workshop ==

[https://www.netbiolab.org/wiki/images/7/7b/2017_BIML_0216_2.zip BIML2017 practice 2 PPT file & python scripts]

[http://www.netbiolab.org/wiki/images/4/4b/Practice1.pdf BIML2016 practice 1 PPT file]

[http://www.netbiolab.org/wiki/images/c/c0/Biml_python_scripts.zip BIML2016 practice 2 python scripts]

<div>{{#widget:AddHtml|content=<img src="../wiki/wordcloud_2013_2017.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div>

Teaching

2019-03-26T08:04:00Z

Dreadcupper:

== Teaching materials for Experiment in microbiology and biochemical engineering laboratory Course ==
[//https://netbiolab.org/w/File:2019_nbl_experiment.pdf 2019 netbiolab experiment teaching material]

[//https://netbiolab.org/w/File:2019_%EC%88%98%EC%97%85%EC%9E%90%EB%A3%8C.zip 2019 netbiolab experiment teaching material]

== Teaching materials for Yonsei Bioinformatics Course ==
[//netbiolab.org/wiki/Kallisto_materials.zip 2018 Bioinformatics Kallisto Practice]

[//netbiolab.org/wiki/WebMev_materials.zip 2018 Bioinformatics WebMeV Practice]

[//netbiolab.org/wiki/Bioinformatics_Machine_Learning_Practice.zip 2018 Bioinformatics Machine Learning Practice]

== Teaching materials for BIML workshop ==

[https://www.netbiolab.org/wiki/images/7/7b/2017_BIML_0216_2.zip BIML2017 practice 2 PPT file & python scripts]

[http://www.netbiolab.org/wiki/images/4/4b/Practice1.pdf BIML2016 practice 1 PPT file]

[http://www.netbiolab.org/wiki/images/c/c0/Biml_python_scripts.zip BIML2016 practice 2 python scripts]

<div>{{#widget:AddHtml|content=<img src="../wiki/wordcloud_2013_2017.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div>

File:2019 nbl experiment.pdf

2019-03-26T08:01:28Z

Dreadcupper:

2018-08-13T05:27:14Z

Dreadcupper:

Journal Club

2018-05-07T06:14:27Z

Dreadcupper:

{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2018
|-
!scope="col" style="padding:.4em" |Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
|-
|style="padding:.4em;" rowspan=2|2018/06/14
|style="padding:.4em;"|18-12
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=A+pan-cancer+analysis+of+enhancer+expression+in+nearly+9000+patient+samples A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.]
|-
|style="padding:.4em;"|18-11
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Machine+learning+identifies+stemness+features+associated+with+oncogenic+dedifferentiation Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.]
|-
|style="padding:.4em;" rowspan=2|2018/06/07
|style="padding:.4em;"|18-10
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Developmental+and+oncogenic+programs+in+H3K27M+gliomas+dissected+by+single-cell+RNA-seq Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq.]
|-
|style="padding:.4em;"|18-9
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Chemoresistance+evolution+in+triple-negative+breast+cancer+delineated+by+single-cell+sequencing Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing.]
|-
|style="padding:.4em;" rowspan=2|2018/05/31
|style="padding:.4em;"|18-8
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Mapping+human+pluripotent+stem+cell+differentiation+pathways+using+high+throughput+single-cell+RNA-sequencing Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing.]
|-
|style="padding:.4em;"|18-7
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=A+single-cell+RNA-seq+survey+of+the+developmental+landscape+of+the+human+prefrontal+cortex A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex.]
|-
|style="padding:.4em;" rowspan=2|2018/05/24
|style="padding:.4em;"|18-6
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Single-cell+RNA+sequencing+identifies+celltype-specific+cis-eQTLs+and+co-expression+QTLs Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs.]
|-
|style="padding:.4em;"|18-5
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=FOCS%3A+a+novel+method+for+analyzing+enhancer+and+gene+activity+patterns+infers+an+extensive+enhancer-promoter+map FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map.]
|-
|style="padding:.4em;" rowspan=2|2018/05/17
|style="padding:.4em;"|18-4
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/29149608 A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.]
|-
|style="padding:.4em;"|18-3
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/29610481 A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.]
|-
|style="padding:.4em;" rowspan=2|2018/05/10
|style="padding:.4em;"|18-2
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Inferring+regulatory+element+landscapes+and+transcription+factor+networks+from+cancer+methylomes Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.]
|-
|style="padding:.4em;"|18-1
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/28129544 Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma.]
|}
{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2017
|-
!scope="col" style="padding:.4em" |Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
|-
|style="padding:.4em;" rowspan=2|2017/06/28
|style="padding:.4em;"|17-36
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/28104840 Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy.]
|-
|style="padding:.4em;"|17-35
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27240091 Landscape of tumor-infiltrating T cell repertoire of human cancers.]
|-
|style="padding:.4em;" rowspan=2|2017/06/14
|style="padding:.4em;"|17-34
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2015/09/01/025908 The landscape of T cell infiltration in human cancer and its association with antigen presenting gene expression.]
|-
|style="padding:.4em;"|17-33
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.08.052 A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.]
|-
|style="padding:.4em;" rowspan=2|2017/06/07
|style="padding:.4em;"|17-32
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.tandfonline.com/doi/full/10.1080/2162402X.2016.1253654 Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis.]
|-
|style="padding:.4em;"|17-31
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.celrep.2016.03.075 Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.]
|-
|style="padding:.4em;" rowspan=2|2017/05/31
|style="padding:.4em;"|17-30
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.02.065 Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma.]
|-
|style="padding:.4em;"|17-29
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.celrep.2016.12.019 Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade.]
|-
|style="padding:.4em;" rowspan=2|2017/05/24
|style="padding:.4em;"|17-28
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.12.022 Systemic Immunity Is Required for Effective Cencer Immunotherapy.]
|-
|style="padding:.4em;"|17-27
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.10.020 Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.]
|-
|style="padding:.4em;" rowspan=2|2017/05/17
|style="padding:.4em;"|17-26
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.10.018 Host and Environmental Factors Influencing Individual Human Cytokine Responses.]
|-
|style="padding:.4em;"|17-25
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.10.017 A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans.]
|-
|style="padding:.4em;" rowspan=2|2017/04/26
|style="padding:.4em;"|17-24
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1038%2FNMETH.4177 Pooled CRISPR screening with single-cell transcriptome readout.]
|-
|style="padding:.4em;"|17-23
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.11.039 Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq.]
|-
|style="padding:.4em;" rowspan=2|2017/04/12
|style="padding:.4em;"|17-22
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.11.038 Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.]
|-
|style="padding:.4em;"|17-21
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1038%2Fnbt.3569 Wishbone identifies bifurcating developmental trajectories from single-cell data.]
|-
|style="padding:.4em;" rowspan=2|2017/04/05
|style="padding:.4em;"|17-20
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2017/02/21/110668 Reversed graph embedding resolves complex single-cell developmental trajectories.]
|-
|style="padding:.4em;"|17-19
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1038%2Fnmeth.4150 Single-cell mRNA quantification and differential analysis with Census.]
|-
|style="padding:.4em;" rowspan=2|2017/03/29
|style="padding:.4em;"|17-18
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.celrep.2016.12.060 Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage.]
|-
|style="padding:.4em;"|17-17
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/26051941 Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis.]
|-
|style="padding:.4em;" rowspan=2|2017/03/22
|style="padding:.4em;"|17-16
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27580035 Single-cell analysis of mixed-lineage states leading to a binary cell fate choice.]
|-
|style="padding:.4em;"|17-15
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27281220 Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq.]
|-
|style="padding:.4em;" rowspan=2|2017/03/15
|style="padding:.4em;"|17-14
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1126%2Fscience.aad0501 Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.]
|-
|style="padding:.4em;"|17-13
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/26084335 Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells.]
|-
|style="padding:.4em;" rowspan=2|2017/02/28
|style="padding:.4em;"|17-12
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27824113 A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions.]
|-
|style="padding:.4em;"|17-11
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[//pubmed.gov/27851969 Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types.]
|-
|style="padding:.4em;" rowspan=2|2017/02/21
|style="padding:.4em;"|17-10
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2016/12/30/097451 Convergence of dispersed regulatory mutations predicts driver genes in prostate cancer.]
|-
|style="padding:.4em;"|17-09
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[//pubmed.gov/27723759 Chromatin structure-based prediction of recurrent noncoding mutations in cancer.]
|-
|style="padding:.4em;" rowspan=2|2017/02/07
|style="padding:.4em;"|17-08
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2016/11/17/088286 Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade.]
|-
|style="padding:.4em;"|17-07
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2016/11/28/090134 Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer.]
|-
|style="padding:.4em;" rowspan=1|2017/01/31
|style="padding:.4em;"|17-06
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/27912059 Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations.]
|-
|style="padding:.4em;" rowspan=1|2017/01/24
|style="padding:.4em;"|17-05
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/27851914 Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells.]
|-
|style="padding:.4em;" rowspan=2|2017/01/17
|style="padding:.4em;"|17-04
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/25938943 Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C]
|-
|style="padding:.4em;"|17-03
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/27306882 CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.]
|-
|style="padding:.4em;" rowspan=1|2017/01/10
|style="padding:.4em;"|17-02
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/26527291 ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis]
|-
|style="padding:.4em;" rowspan=1|2017/01/03
|style="padding:.4em;"|17-01
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/26287467 Single-cell messenger RNA sequencing reveals rare intestinal cell types]
|-
|}
{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2016
|-
!scope="col" style="padding:.4em" |Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
|-
|style="padding:.4em;" rowspan=1|2016/12/27
|style="padding:.4em;"|2016-31
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/25664528 Decoding the regulatory network of early blood development from single-cell gene expression measurements.]
|-
|style="padding:.4em;" rowspan=1|2016/12/6
|style="padding:.4em;"|2016-30
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26299571 Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.]
|-
|style="padding:.4em;" rowspan=1|2016/11/29
|style="padding:.4em;"|2016-29
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/24658644 The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.]
|-
|style="padding:.4em;" rowspan=1|2016/11/22
|style="padding:.4em;"|2016-28
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26887813 Classification of low quality cells from single-cell RNA-seq data.]
|-
|style="padding:.4em;" rowspan=1|2016/11/15
|style="padding:.4em;"|2016-27
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26000487 Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.]
|-
|style="padding:.4em;" rowspan=1|2016/11/8
|style="padding:.4em;"|2016-26
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26000488 Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.]
|-
|style="padding:.4em;" rowspan=1|2016/11/1
|style="padding:.4em;"|2016-25
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27426982 Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.]
|-
|style="padding:.4em;" rowspan=1|2016/10/25
|style="padding:.4em;"|2016-24
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27549193 Comprehensive analyses of tumor immunity: implications for cancer immunotherapy.]
|-
|style="padding:.4em;" rowspan=1|2016/10/11
|style="padding:.4em;"|2016-23
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=sidespread+parainflammation Widespread parainflammation in human cancer]
|-
|style="padding:.4em;" rowspan=1|2016/9/27
|style="padding:.4em;"|2016-22
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27535533 Analysis of protein-coding genetic variation in 60,706 humans]
|-
|style="padding:.4em;" rowspan=1|2016/9/20
|style="padding:.4em;"|2016-21
|style="padding:.4em;"|SM Yang
|style="padding:.4em;text-align:left"|
Functional characterization of somatic mutations in cancer using network-based inference of protein activity
[http://www.ncbi.nlm.nih.gov/pubmed/27322546 pubmed]
[http://www.nature.com/ng/journal/v48/n8/full/ng.3593.html fulltext]
|-
|style="padding:.4em;" rowspan=1|2016/9/13
|style="padding:.4em;"|2016-20
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=exploiting+single-cell+expression+to+characterize Exploiting single-cell expression to characterize co-expression replicability.]
|-
|style="padding:.4em;" rowspan=1|2016/9/6
|style="padding:.4em;"|2016-19
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26940869 Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade]
|-
|style="padding:.4em;" rowspan=1|2016/8/31
|style="padding:.4em;"|2016-18
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27264179 A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors]
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|style="padding:.4em;" rowspan=1|2016/8/16
|style="padding:.4em;"|2016-17
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27309802 The landscape of accessible chromatin in mammalian preimplantation embryos]
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|style="padding:.4em;" rowspan=1|2016/8/8
|style="padding:.4em;"|2016-16
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27064255 Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin]
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|style="padding:.4em;" rowspan=1|2016/8/1
|style="padding:.4em;"|2016-15
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27040498 Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients]
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|style="padding:.4em;" rowspan=1|2016/7/25
|style="padding:.4em;"|2016-14
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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]
|-
|style="padding:.4em;" rowspan=1|2016/7/18
|style="padding:.4em;"|2016-13
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]
|-
|style="padding:.4em;" rowspan=2|2016/6/8
|style="padding:.4em;"|2016-12
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]
|-
|style="padding:.4em;"| 2016-11
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]
|-
|style="padding:.4em;" rowspan=2|2016/6/1
|style="padding:.4em;"|2016-10
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]
|-
|style="padding:.4em;"| 2016-9
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]
|-
|style="padding:.4em;" rowspan=2|2016/5/18
|style="padding:.4em;"|2016-8
|style="padding:.4em;"|CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]
|-
|style="padding:.4em;"| 2016-7
|style="padding:.4em;"| CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]
|-
|style="padding:.4em;" rowspan=2|2016/5/11
|style="padding:.4em;"|2016-6
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]
|-
|style="padding:.4em;"| 2016-5
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]
|-
|style="padding:.4em;" rowspan=2|2016/5/4
|style="padding:.4em;"|2016-4
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[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]
|-
|style="padding:.4em;"| 2016-3
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]
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|style="padding:.4em;" rowspan=2|2016/4/27
|style="padding:.4em;"|2016-2
|style="padding:.4em;"|CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]
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|style="padding:.4em;"| 2016-1
|style="padding:.4em;"| CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]
|}

{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2015
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!scope="col" style="padding:.4em" | Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
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|style="padding:.4em;" rowspan=2|2015/06/11
|style="padding:.4em;"|2015-55
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]
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|style="padding:.4em;"|2015-54
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;" rowspan=2|2015/06/04
|style="padding:.4em;"|2015-53
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]
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|style="padding:.4em;"|2015-52
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]
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|style="padding:.4em;" rowspan=2|2015/05/28
|style="padding:.4em;"|2015-51
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2015-50
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]
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|style="padding:.4em;" rowspan=2|2015/05/21
|style="padding:.4em;"|2015-49
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]
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|style="padding:.4em;"|2015-48
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]
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|style="padding:.4em;" rowspan=2|2015/05/14
|style="padding:.4em;"|2015-47
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]
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|style="padding:.4em;"|2015-46
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]
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|style="padding:.4em;" rowspan=3|2015/05/07
|style="padding:.4em;"|2015-45
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]
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|style="padding:.4em;"|2015-44
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]
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|style="padding:.4em;"|2015-43
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]

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|style="padding:.4em;" rowspan=2|2015/04/30
|style="padding:.4em;"|2015-42
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]
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|style="padding:.4em;"|2015-41
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]
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|style="padding:.4em;" rowspan=3|2015/04/23
|style="padding:.4em;"|2015-40
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]
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|style="padding:.4em;"|2015-39
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]
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|style="padding:.4em;"|2015-38
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]
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|style="padding:.4em;" rowspan=2|2015/04/09
|style="padding:.4em;"|2015-37
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]
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|style="padding:.4em;"|2015-36
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]
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|style="padding:.4em;" rowspan=2|2015/04/02
|style="padding:.4em;"|2015-35
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]
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|style="padding:.4em;"|2015-34
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]
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|style="padding:.4em;" rowspan=2|2015/03/26
|style="padding:.4em;"|2015-33
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]
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|style="padding:.4em;"|2015-32
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;" rowspan=2|2015/03/19
|style="padding:.4em;"|2015-31
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2015-30
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]
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|style="padding:.4em;" rowspan=3|2015/03/12
|style="padding:.4em;"|2015-29
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]
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|style="padding:.4em;"|2015-28
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]
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|style="padding:.4em;"|2015-27
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]
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|style="padding:.4em;" rowspan=3|2015/03/09
|style="padding:.4em;"|2015-26
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]
|-
|style="padding:.4em;"|2015-25
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|
[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.]
|-
|style="padding:.4em;"|2015-24
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]
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|style="padding:.4em;" rowspan=3|2015/03/02
|style="padding:.4em;"|2015-23
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]
|-
|style="padding:.4em;"|2015-22
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2015-21
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]
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|style="padding:.4em;" rowspan=3|2015/02/24
|style="padding:.4em;"|2015-20
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]
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|style="padding:.4em;"|2015-19
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]
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|style="padding:.4em;"|2015-18
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]
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|style="padding:.4em;" rowspan=3|2015/02/16
|style="padding:.4em;"|2015-17
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]
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|style="padding:.4em;"|2015-16
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]
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|style="padding:.4em;"|2015-15
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]
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|style="padding:.4em;" rowspan=4|2015/02/02
|style="padding:.4em;"|2015-14
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]
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|style="padding:.4em;"|2015-13
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]
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|style="padding:.4em;"|2015-12
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]
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|style="padding:.4em;"|2015-11
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;" rowspan=5|2015/01/26
|style="padding:.4em;"|2015-10
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]
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|style="padding:.4em;"|2015-09
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]
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|style="padding:.4em;"|2015-08
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]
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|style="padding:.4em;"|2015-07
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]
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|style="padding:.4em;"|2015-06
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]
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|style="padding:.4em;" rowspan=3|2015/01/12
|style="padding:.4em;"|2015-05
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]
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|style="padding:.4em;"|2015-04
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]
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|style="padding:.4em;"|2015-03
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]
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|style="padding:.4em;" rowspan=2|2015/01/05
|style="padding:.4em;"|2015-02
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]
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|style="padding:.4em;"|2015-01
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[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.]
|}
{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2014
|-
!scope="col" style="padding:.4em" | Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
|-
|style="padding:.4em;" rowspan=2|2014/12/23
|style="padding:.4em;"|2014-41
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]
|-
|style="padding:.4em;"|2014-40
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]
|-
|style="padding:.4em;" rowspan=4|2014/12/09
|style="padding:.4em;"|2014-39
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]
|-
|style="padding:.4em;"|2014-38
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]
|-
|style="padding:.4em;"|2014-37
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]
|-
|style="padding:.4em;"|2014-36
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]
|-
|style="padding:.4em;" rowspan=2|2014/12/02
|style="padding:.4em;"|2014-35
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]
|-
|style="padding:.4em;"|2014-34
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]
|-
|style="padding:.4em;" rowspan=2|2014/11/25
|style="padding:.4em;"|2014-33
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[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.]
|-
|style="padding:.4em;"|2014-32
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]
|-
|style="padding:.4em;" rowspan=2|2014/11/18
|style="padding:.4em;"|2014-31
|style="padding:.4em;"|SM Yang
|style="padding:.4em;text-align:left"|
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]
|-
|style="padding:.4em;"|2014-30
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]
|-
|style="padding:.4em;" rowspan=3|2014/11/11
|style="padding:.4em;"|2014-29
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]
|-
|style="padding:.4em;"|2014-28
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]
|-
|style="padding:.4em;"|2014-27
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]
|-
|style="padding:.4em;" rowspan=2|2014/11/04
|style="padding:.4em;"|2014-26
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]
|-
|style="padding:.4em;"|2014-25
|style="padding:.4em;"|JH Shin
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]
|-
|style="padding:.4em;" rowspan=2|2014/10/28
|style="padding:.4em;"|2014-24
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]
|-
|style="padding:.4em;"|2014-23
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[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.]
|-
|style="padding:.4em;" rowspan=2|2014/09/30
|style="padding:.4em;"|2014-22
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]
|-
|style="padding:.4em;"|2014-21
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]
|-
|style="padding:.4em;" rowspan=2|2014/09/23
|style="padding:.4em;"|2014-20
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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.]
|-
|style="padding:.4em;"|2014-19
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]
|-
|style="padding:.4em;" rowspan=2|2014/09/16
|style="padding:.4em;"|2014-18
|style="padding:.4em;"|JH Shin
|style="padding:.4em;text-align:left"|
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]
|-
|style="padding:.4em;"|2014-17
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]
|-
|style="padding:.4em;" rowspan=2|2014/09/02
|style="padding:.4em;"|2014-16
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]
|-
|style="padding:.4em;"|2014-15
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]
|-
|style="padding:.4em;" rowspan=2|2014/08/19
|style="padding:.4em;"|2014-14
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]
|-
|style="padding:.4em;"|2014-13
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]
|-
|style="padding:.4em;" rowspan=2|2014/08/12
|style="padding:.4em;"|2014-12
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]
|-
|style="padding:.4em;"|2014-11
|style="padding:.4em;"|HJ Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]
|-
|style="padding:.4em;" rowspan=2|2014/08/05
|style="padding:.4em;"|2014-10
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]
|-
|style="padding:.4em;"|2014-9
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]
|-
|style="padding:.4em;" rowspan=3|2014/07/29
|style="padding:.4em;"|2014-8
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]
|-
|style="padding:.4em;"|2014-7
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]
|-
|style="padding:.4em;"|2014-6
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]
|-
|style="padding:.4em;" rowspan=3|2014/07/22
|style="padding:.4em;"|2014-5
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]
|-
|style="padding:.4em;"|2014-4
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]
|-
|style="padding:.4em;"|2014-3
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]
|-
|style="padding:.4em;" rowspan=2|2014/07/15
|style="padding:.4em;"|2014-2
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]
|-
|style="padding:.4em;"|2014-1
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]
|}
{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2013
|-
!scope="col" style="padding:.4em" | Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
|-
|style="padding:.4em;" rowspan=2|2013/06/26
|style="padding:.4em;"|2013-31
|style="padding:.4em;"|HJ Han
|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]
|-
|style="padding:.4em;"|2013-30
|style="padding:.4em;"|YH Ko
|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]
|-
|style="padding:.4em;" rowspan=2|2013/06/04
|style="padding:.4em;"|2013-29
|style="padding:.4em;"|KS Kim
|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]
|-
|style="padding:.4em;"|2013-28
|style="padding:.4em;"|ER Kim
|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]
|-
|style="padding:.4em;" rowspan=2|2013/05/28
|style="padding:.4em;"|2013-27
|style="padding:.4em;"|YH Ko
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]
|-
|style="padding:.4em;"|2013-26
|style="padding:.4em;"|JE Shim
|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]
|-
|style="padding:.4em;" rowspan=2|2013/05/21
|style="padding:.4em;"|2013-25
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]
|-
|style="padding:.4em;"|2013-24
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]

|-
|style="padding:.4em;" rowspan=2|2013/05/14
|style="padding:.4em;"|2013-23
|style="padding:.4em;"|JE Shim
|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]

|-
|style="padding:.4em;"|2013-22
|style="padding:.4em;"|HJ Kim
|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]
|-
|style="padding:.4em;" rowspan=2|'''2013/05/07'''
|style="padding:.4em;"|2013-21
|style="padding:.4em;"|ER Kim
|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]
|-
|style="padding:.4em;"|2013-20
|style="padding:.4em;"|HS Shim
|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]
|-
|style="padding:.4em;"|2013/04/09
|style="padding:.4em;"|2013-19
|style="padding:.4em;"|HJ Kim
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]
|-
|style="padding:.4em;"|2013/04/02
|style="padding:.4em;"|2013-18
|style="padding:.4em;"|HJ Kim
|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]
|-
|style="padding:.4em;" |2013/03/12
|style="padding:.4em;"|2013-17
|style="padding:.4em;"| ER Kim
|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]
|-
|style="padding:.4em;" rowspan=1|2013/03/05
|style="padding:.4em;"|2013-16
|style="padding:.4em;"| ER Kim
|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]
|-
|style="padding:.4em;" rowspan=3|2013/02/21
|style="padding:.4em;"|2013-15
|style="padding:.4em;"| KS Kim
|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]
|-
|style="padding:.4em;"|2013-14
|style="padding:.4em;"| KS Kim
|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]
|-
|style="padding:.4em;"|2013-13
|style="padding:.4em;"| HJ Han
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]
|-
|style="padding:.4em;" rowspan=3|2013/02/15
|style="padding:.4em;"|2013-12
|style="padding:.4em;"| HJ Han
|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]
|-
|style="padding:.4em;"|2013-11
|style="padding:.4em;"| JE Shim, CY Kim
|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]
|-
|style="padding:.4em;"|2013-10
|style="padding:.4em;"|HJ Han, JH Kim
|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]
|-
|style="padding:.4em;" rowspan=3|2013/02/08
|style="padding:.4em;"|2013-09
|style="padding:.4em;"|HJ Kim
|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]
|-
|style="padding:.4em;"|2013-08
|style="padding:.4em;"|JE Shim, CY Kim
|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]
|-
|style="padding:.4em;"|2013-07
|style="padding:.4em;"|HJ Han, JH Kim
|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]
|-
|style="padding:.4em;" rowspan=3|2013/01/25
|style="padding:.4em;"|2013-06
|style="padding:.4em;"|HJ Han, '''JH Kim'''
|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]
|-
|style="padding:.4em;"|2013-05
|style="padding:.4em;"|'''ER Kim''', HS Shim
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]
|-
|style="padding:.4em;"|2013-04
|style="padding:.4em;"|'''HJ Han''', JH Kim
|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]

|-
|style="padding:.4em;" rowspan=2|2013/01/18
|style="padding:.4em;"|2013-03
|style="padding:.4em;"|KS Kim, '''TH Kim'''
|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]
|-
|style="padding:.4em;"|2013-02
|style="padding:.4em;"|'''HJ Han''', JH Kim
|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]
|-
|style="padding:.4em;" rowspan=1|2013/01/11
|style="padding:.4em;"|2013-01
|style="padding:.4em;"| '''JE Shim''', CY Kim
|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]
|}

2012
{|border ="1"
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title
|-
|rowspan = "1"|2013/01/11
|align ="center"|2012-81
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]
|-
|rowspan = "1"|2012/12/04
|align ="center"|2012-80
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]
|-
|rowspan = "2"|2012/11/20
| align="center"|2012-79
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]
|-
| align="center"|2012-78
|[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]
|-
|rowspan = "2"|2012/11/06
| align="center"|2012-77
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]
|-
| align="center"|2012-76
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes]
|-
|rowspan = "6" |2012/07/19
| align="center"|2012-75
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]
|-
| align="center"|2012-74
|[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]
|-
| align="center"|2012-73
|[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]
|-
| align="center"|2012-72
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]
|-
| align="center"|2012-71
|[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]
|-
| align="center"|2012-70
|[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]
|-
|rowspan = "8" |2012/07/16
| align="center"|2012-69
|[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]
|-
| align="center"|2012-66
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]
|-
| align="center"|2012-65
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]
|-
| align="center"|2012-64
|[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]
|-
|align="center"|2012-63
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]
|-
|align="center"|2012-62
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]
|-
|align="center"|2012-61
|[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]
|-
|align="center"|2012-60
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]
|-
|rowspan = "3" |2012/07/13
|align="center"|2012-59
|[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]
|-
| align="center"|2012-58
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]
|-
|align="center"|2012-57
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]
|-
|rowspan = "4" |2012/07/12
|align="center"|2012-56
|[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]
|-
|align="center"|2012-55
|[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]
|-
| align="center"|2012-54
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]
|-
|align="center"|2012-53
|[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]
|-
|rowspan = "6" |2012/07/09
|align="center"|2012-52
|[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]
|-
|align="center"|2012-51
|[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]
|-
| align="center"|2012-50
|[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]
|-
|align="center"|2012-49
|[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]
|-
|align="center"|2012-48
|[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]
|-
|align="center"|2012-47
|[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]
|-
|rowspan = "6" |2012/07/06
| align="center"|2012-46
|[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)]
|-
|align="center"|2012-45
|[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]
|-
|align="center"|2012-44
|[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]
|-
|align="center"|2012-43
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]
|-
| align="center"|2012-42
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]
|-
|align="center"|2012-41
|[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]
|-
|rowspan = "6" |2012/07/02
|align="center"|2012-40
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]
|-
|align="center"|2012-39
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]
|-
| align="center"|2012-38
|[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]
|-
|align="center"|2012-37
|[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]
|-
|align="center"|2012-36
|[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]
|-
|align="center"|2012-35
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]
|-
|rowspan = "3" |2012/03/05
| align="center"|2012-34
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]
|-
|align="center"|2012-33
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]
|-
|align="center"|2012-32
|[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 ]
|-
|rowspan = "7" |2012/02/27<br />2012/02/28
| align="center"|2012-31
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]
|-
|align="center"|2012-30
|[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]
|-
|align="center"|2012-29
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]
|-
|align="center"|2012-28
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]
|-
|align="center"|2012-27
|[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]
|-
|align="center"|2012-26
|[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]
|-
|align="center"|2012-25
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]
|-
|rowspan = "5" |2012/02/06
| align="center"|2012-24
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]
|-
|align="center"|2012-23
|[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]
|-
|align="center"|2012-22
|[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]
|-
|align="center"|2012-21
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]
|-
|align="center"|2012-20
|[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]
|-
|rowspan = "5" |2012/01/30
|align="center"|2012-19
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]
|-
|align="center"|2012-18
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]
|-
|align="center"|2012-17
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]
|-
|align="center"|2012-16
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]
|-
|align="center"|2012-15
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]
|-
|rowspan = "3" |2012/01/09
|align="center"|2012-14
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]
|-
|align="center"|2012-13
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]
|-
|align="center"|2012-12
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]
|-
|rowspan = "6" |2012/01/09<br />2012/01/16
| align="center"|2012-11
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]
|-
|align="center"|2012-10
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]
|-
|align="center"|2012-09
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]
|-
|align="center"|2012-08
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]
|-
|align="center"|2012-07
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]
|-
|align="center"|2012-06
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]
|-
|rowspan = "3" |2012/01/09<br />2012/01/16
|align="center"|2012-05
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]
|-
|align="center"|2012-04
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]
|-
|align="center"|2012-03
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]
|-
|rowspan = "2" |2012/01/09<br />2012/01/16
|align="center"|2012-02
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]
|-
|align="center"|2012-01
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]
|}
2011
{|border ="1"
|style="color:black; background-color:#dcdcdc;" align="center" |Date
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title
|-
|rowspan = "6" |2011/11/28
|align="center"|2011-49
|[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]
|-
|align="center"|2011-48
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]
|-
|align="center"|2011-47
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]
|-
|align="center"|2011-46
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]
|-
|align="center"|2011-45
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]
|-
|align="center"|2011-44
|[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]
|-
|rowspan = "3" |2011/11/14
|align="center"|2011-43
|[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]
|-
|align="center"|2011-42
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]
|-
|align="center"|2011-41
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]
|-
|rowspan = "4" |2011/11/07
|align="center"|2011-40
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]
|-
|align="center"|2011-39
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]
|-
|align="center"|2011-38
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]
|-
|align="center"|2011-37
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]
|-
|rowspan = "3" |2011/11/07
|align="center"|2011-36
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]
|-
|align="center"|2011-35
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]
|-
|align="center"|2011-34
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]
|-
|rowspan = "3" |2011/10/05
|align="center"|2011-33
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]
|-
|align="center"|2011-32
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]
|-
|align="center"|2011-31
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]
|-
|rowspan = "4" |2011/10/04
|align="center"|2011-30
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]
|-
|align="center"|2011-29
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]
|-
|align="center"|2011-28
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]
|-
|align="center"|2011-27
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]
|-
|rowspan = "2" |2011/09/19
|align="center"|2011-26
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]
|-
|align="center"|2011-25
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]
|-
|rowspan = "2" |2011/09/05
|align="center"|2011-24
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]
|-
|align="center"|2011-23
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]
|-
|rowspan = "2" |2011/09/22
|align="center"|2011-22
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]
|-
|align="center"|2011-21
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]
|-
|2011/06/20
|align="center"|2011-20
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]
|-
|rowspan = "2" |2011/03/30
|align="center"|2011-19
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]
|-
|align="center"|2011-18
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]
|-
|rowspan = "2" |2011/03/16
|align="center"|2011-17
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']
|-
|align="center"|2011-16
|[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]
|-
|rowspan = "3" |2011/04/25
|align="center"|2011-15
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]
|-
|align="center"|2011-14
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]
|-
|align="center"|2011-13
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]
|-
|rowspan = "2" |2011/04/11
|align="center"|2011-12
|[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]
|-
|align="center"|2011-11
|***Changed!***
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]
|-
|rowspan = "2"|2011/03/28
|align="center"|2011-10
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]
|-
|align="center"|2011-09
|[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"|2011/03/14
|align="center"|2011-08
|[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]
|-
|align="center"|2011-07
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]
|-
|rowspan = "2"|2011/02/28
|align="center"|2011-06
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]
|-
|align="center"|2011-05
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]
|-
|2011/02/21
|align="center"|2011-04
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]
|-
|2011/02/14
|align="center"|2011-03
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]
|-
|rowspan = "2"|2011/01/31
|align="center"|2011-02
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]
|-
|align="center"|2011-01
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]
|}
2010
{|border ="1"
|style="color:black; background-color:#dcdcdc;" align="center" |Date
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title
|-
|rowspan = "2"|2010/12/27
|align="center"|2010-29
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]
|-
|align="center"|2010-28
|[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"|2010/11/15
|align="center"|2010-27
|[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]
|-
|align="center"|2010-26
|[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"|2010/11/01
|align="center"|2010-25
|[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]
|-
|align="center"|2010-24
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]
|-
|2010/10/11
|align="center"|2010-23
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]
|-
|rowspan = "2"|2010/09/13
|align="center"|2010-22
|[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]
|-
|align="center"|2010-21
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]
|-
|2010/05/26
|align="center"|2010-20
|[[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]]
|-
|2010/05/19
|align="center"|2010-19
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]
|-
|2010/04/21
|align="center"|2010-18
|[[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]]
|-
|2010/04/14
|align="center"|2010-17
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]
|-
|rowspan = "2" |2010/04/07
|align="center"|2010-16
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]
|-
|align="center"|2010-15
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]
|-
|rowspan="2"|2010/03/31
|align="center"|2010-14
|[[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]]
|-
|align="center"|2010-13
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]
|-
|2010/03/24
|align="center"|2010-12
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]
|-
|2010/01/18
|align="center"|2010-11
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies
|-
|2010/01/16
|align="center"|2010-10
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells
|-
|2010/01/15
|align="center"|2010-09
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions
|-
|2010/01/14
|align="center"|2010-08
|chemogenomic_profiling_predicts_antifungal_synergies
|-
|2010/01/13
|align="center"|2010-07
|edgetic_perturbation_models_of_human_inherited_disorders
|-
|2010/01/12
|align="center"|2010-06
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans
|-
|2010/01/11
|align="center"|2010-05
|predicting_new_molecular_targets_for_known_drugs.pdf
Reference:SEA(Similarity Ensemble Approach)
|-
|2010/01/09
|align="center"|2010-04
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance
|-
|2010/01/08
|align="center"|2010-03
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer
|-
|2010/01/07
|align="center"|2010-02
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network
|-
|2010/01/06
|align="center"|2010-01
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs
|}

Journal Club

2018-05-07T06:13:42Z

Dreadcupper:

{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2018
|-
!scope="col" style="padding:.4em" |Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
|-
|style="padding:.4em;" rowspan=2|2018/06/14
|style="padding:.4em;"|18-12
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=A+pan-cancer+analysis+of+enhancer+expression+in+nearly+9000+patient+samples A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.]
|-
|style="padding:.4em;"|18-11
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Machine+learning+identifies+stemness+features+associated+with+oncogenic+dedifferentiation Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.]
|-
|style="padding:.4em;" rowspan=2|2018/06/07
|style="padding:.4em;"|18-10
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Developmental+and+oncogenic+programs+in+H3K27M+gliomas+dissected+by+single-cell+RNA-seq Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq.]
|-
|style="padding:.4em;"|18-9
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Chemoresistance+evolution+in+triple-negative+breast+cancer+delineated+by+single-cell+sequencing Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing.]
|-
|style="padding:.4em;" rowspan=2|2018/05/31
|style="padding:.4em;"|18-8
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Mapping+human+pluripotent+stem+cell+differentiation+pathways+using+high+throughput+single-cell+RNA-sequencing Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing.]
|-
|style="padding:.4em;"|18-7
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=A+single-cell+RNA-seq+survey+of+the+developmental+landscape+of+the+human+prefrontal+cortex A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex.]
|-
|style="padding:.4em;" rowspan=2|2018/05/24
|style="padding:.4em;"|18-6
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Single-cell+RNA+sequencing+identifies+celltype-specific+cis-eQTLs+and+co-expression+QTLs Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs.]
|-
|style="padding:.4em;"|18-5
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=FOCS%3A+a+novel+method+for+analyzing+enhancer+and+gene+activity+patterns+infers+an+extensive+enhancer-promoter+map FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map.]
|-
|style="padding:.4em;" rowspan=2|2018/05/17
|style="padding:.4em;"|18-4
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/29149608 A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.]
|-
|style="padding:.4em;"|18-3
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/29610481 A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.]
|-
|style="padding:.4em;" rowspan=2|2018/05/20
|style="padding:.4em;"|18-2
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Inferring+regulatory+element+landscapes+and+transcription+factor+networks+from+cancer+methylomes Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.]
|-
|style="padding:.4em;"|18-1
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/28129544 Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma.]
|}
{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2017
|-
!scope="col" style="padding:.4em" |Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
|-
|style="padding:.4em;" rowspan=2|2017/06/28
|style="padding:.4em;"|17-36
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/28104840 Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy.]
|-
|style="padding:.4em;"|17-35
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27240091 Landscape of tumor-infiltrating T cell repertoire of human cancers.]
|-
|style="padding:.4em;" rowspan=2|2017/06/14
|style="padding:.4em;"|17-34
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2015/09/01/025908 The landscape of T cell infiltration in human cancer and its association with antigen presenting gene expression.]
|-
|style="padding:.4em;"|17-33
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.08.052 A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.]
|-
|style="padding:.4em;" rowspan=2|2017/06/07
|style="padding:.4em;"|17-32
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.tandfonline.com/doi/full/10.1080/2162402X.2016.1253654 Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis.]
|-
|style="padding:.4em;"|17-31
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.celrep.2016.03.075 Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.]
|-
|style="padding:.4em;" rowspan=2|2017/05/31
|style="padding:.4em;"|17-30
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.02.065 Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma.]
|-
|style="padding:.4em;"|17-29
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.celrep.2016.12.019 Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade.]
|-
|style="padding:.4em;" rowspan=2|2017/05/24
|style="padding:.4em;"|17-28
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.12.022 Systemic Immunity Is Required for Effective Cencer Immunotherapy.]
|-
|style="padding:.4em;"|17-27
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.10.020 Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.]
|-
|style="padding:.4em;" rowspan=2|2017/05/17
|style="padding:.4em;"|17-26
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.10.018 Host and Environmental Factors Influencing Individual Human Cytokine Responses.]
|-
|style="padding:.4em;"|17-25
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.10.017 A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans.]
|-
|style="padding:.4em;" rowspan=2|2017/04/26
|style="padding:.4em;"|17-24
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1038%2FNMETH.4177 Pooled CRISPR screening with single-cell transcriptome readout.]
|-
|style="padding:.4em;"|17-23
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.11.039 Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq.]
|-
|style="padding:.4em;" rowspan=2|2017/04/12
|style="padding:.4em;"|17-22
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.11.038 Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.]
|-
|style="padding:.4em;"|17-21
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1038%2Fnbt.3569 Wishbone identifies bifurcating developmental trajectories from single-cell data.]
|-
|style="padding:.4em;" rowspan=2|2017/04/05
|style="padding:.4em;"|17-20
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2017/02/21/110668 Reversed graph embedding resolves complex single-cell developmental trajectories.]
|-
|style="padding:.4em;"|17-19
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1038%2Fnmeth.4150 Single-cell mRNA quantification and differential analysis with Census.]
|-
|style="padding:.4em;" rowspan=2|2017/03/29
|style="padding:.4em;"|17-18
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.celrep.2016.12.060 Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage.]
|-
|style="padding:.4em;"|17-17
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/26051941 Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis.]
|-
|style="padding:.4em;" rowspan=2|2017/03/22
|style="padding:.4em;"|17-16
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27580035 Single-cell analysis of mixed-lineage states leading to a binary cell fate choice.]
|-
|style="padding:.4em;"|17-15
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27281220 Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq.]
|-
|style="padding:.4em;" rowspan=2|2017/03/15
|style="padding:.4em;"|17-14
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1126%2Fscience.aad0501 Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.]
|-
|style="padding:.4em;"|17-13
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/26084335 Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells.]
|-
|style="padding:.4em;" rowspan=2|2017/02/28
|style="padding:.4em;"|17-12
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27824113 A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions.]
|-
|style="padding:.4em;"|17-11
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[//pubmed.gov/27851969 Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types.]
|-
|style="padding:.4em;" rowspan=2|2017/02/21
|style="padding:.4em;"|17-10
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2016/12/30/097451 Convergence of dispersed regulatory mutations predicts driver genes in prostate cancer.]
|-
|style="padding:.4em;"|17-09
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[//pubmed.gov/27723759 Chromatin structure-based prediction of recurrent noncoding mutations in cancer.]
|-
|style="padding:.4em;" rowspan=2|2017/02/07
|style="padding:.4em;"|17-08
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2016/11/17/088286 Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade.]
|-
|style="padding:.4em;"|17-07
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2016/11/28/090134 Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer.]
|-
|style="padding:.4em;" rowspan=1|2017/01/31
|style="padding:.4em;"|17-06
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/27912059 Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations.]
|-
|style="padding:.4em;" rowspan=1|2017/01/24
|style="padding:.4em;"|17-05
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/27851914 Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells.]
|-
|style="padding:.4em;" rowspan=2|2017/01/17
|style="padding:.4em;"|17-04
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/25938943 Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C]
|-
|style="padding:.4em;"|17-03
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/27306882 CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.]
|-
|style="padding:.4em;" rowspan=1|2017/01/10
|style="padding:.4em;"|17-02
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/26527291 ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis]
|-
|style="padding:.4em;" rowspan=1|2017/01/03
|style="padding:.4em;"|17-01
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/26287467 Single-cell messenger RNA sequencing reveals rare intestinal cell types]
|-
|}
{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2016
|-
!scope="col" style="padding:.4em" |Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
|-
|style="padding:.4em;" rowspan=1|2016/12/27
|style="padding:.4em;"|2016-31
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/25664528 Decoding the regulatory network of early blood development from single-cell gene expression measurements.]
|-
|style="padding:.4em;" rowspan=1|2016/12/6
|style="padding:.4em;"|2016-30
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26299571 Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.]
|-
|style="padding:.4em;" rowspan=1|2016/11/29
|style="padding:.4em;"|2016-29
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/24658644 The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.]
|-
|style="padding:.4em;" rowspan=1|2016/11/22
|style="padding:.4em;"|2016-28
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26887813 Classification of low quality cells from single-cell RNA-seq data.]
|-
|style="padding:.4em;" rowspan=1|2016/11/15
|style="padding:.4em;"|2016-27
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26000487 Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.]
|-
|style="padding:.4em;" rowspan=1|2016/11/8
|style="padding:.4em;"|2016-26
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26000488 Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.]
|-
|style="padding:.4em;" rowspan=1|2016/11/1
|style="padding:.4em;"|2016-25
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27426982 Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.]
|-
|style="padding:.4em;" rowspan=1|2016/10/25
|style="padding:.4em;"|2016-24
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27549193 Comprehensive analyses of tumor immunity: implications for cancer immunotherapy.]
|-
|style="padding:.4em;" rowspan=1|2016/10/11
|style="padding:.4em;"|2016-23
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=sidespread+parainflammation Widespread parainflammation in human cancer]
|-
|style="padding:.4em;" rowspan=1|2016/9/27
|style="padding:.4em;"|2016-22
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27535533 Analysis of protein-coding genetic variation in 60,706 humans]
|-
|style="padding:.4em;" rowspan=1|2016/9/20
|style="padding:.4em;"|2016-21
|style="padding:.4em;"|SM Yang
|style="padding:.4em;text-align:left"|
Functional characterization of somatic mutations in cancer using network-based inference of protein activity
[http://www.ncbi.nlm.nih.gov/pubmed/27322546 pubmed]
[http://www.nature.com/ng/journal/v48/n8/full/ng.3593.html fulltext]
|-
|style="padding:.4em;" rowspan=1|2016/9/13
|style="padding:.4em;"|2016-20
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=exploiting+single-cell+expression+to+characterize Exploiting single-cell expression to characterize co-expression replicability.]
|-
|style="padding:.4em;" rowspan=1|2016/9/6
|style="padding:.4em;"|2016-19
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26940869 Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade]
|-
|style="padding:.4em;" rowspan=1|2016/8/31
|style="padding:.4em;"|2016-18
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27264179 A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors]
|-
|style="padding:.4em;" rowspan=1|2016/8/16
|style="padding:.4em;"|2016-17
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27309802 The landscape of accessible chromatin in mammalian preimplantation embryos]
|-
|style="padding:.4em;" rowspan=1|2016/8/8
|style="padding:.4em;"|2016-16
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27064255 Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin]
|-
|style="padding:.4em;" rowspan=1|2016/8/1
|style="padding:.4em;"|2016-15
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27040498 Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients]
|-
|style="padding:.4em;" rowspan=1|2016/7/25
|style="padding:.4em;"|2016-14
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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]
|-
|style="padding:.4em;" rowspan=1|2016/7/18
|style="padding:.4em;"|2016-13
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]
|-
|style="padding:.4em;" rowspan=2|2016/6/8
|style="padding:.4em;"|2016-12
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]
|-
|style="padding:.4em;"| 2016-11
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]
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|style="padding:.4em;" rowspan=2|2016/6/1
|style="padding:.4em;"|2016-10
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]
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|style="padding:.4em;"| 2016-9
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]
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|style="padding:.4em;" rowspan=2|2016/5/18
|style="padding:.4em;"|2016-8
|style="padding:.4em;"|CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]
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|style="padding:.4em;"| 2016-7
|style="padding:.4em;"| CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]
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|style="padding:.4em;" rowspan=2|2016/5/11
|style="padding:.4em;"|2016-6
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]
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|style="padding:.4em;"| 2016-5
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]
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|style="padding:.4em;" rowspan=2|2016/5/4
|style="padding:.4em;"|2016-4
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[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]
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|style="padding:.4em;"| 2016-3
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]
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|style="padding:.4em;" rowspan=2|2016/4/27
|style="padding:.4em;"|2016-2
|style="padding:.4em;"|CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]
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|style="padding:.4em;"| 2016-1
|style="padding:.4em;"| CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]
|}

{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2015
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!scope="col" style="padding:.4em" | Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
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|style="padding:.4em;" rowspan=2|2015/06/11
|style="padding:.4em;"|2015-55
|style="padding:.4em;"|
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[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]
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|style="padding:.4em;"|2015-54
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;" rowspan=2|2015/06/04
|style="padding:.4em;"|2015-53
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]
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|style="padding:.4em;"|2015-52
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]
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|style="padding:.4em;" rowspan=2|2015/05/28
|style="padding:.4em;"|2015-51
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2015-50
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]
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|style="padding:.4em;" rowspan=2|2015/05/21
|style="padding:.4em;"|2015-49
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]
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|style="padding:.4em;"|2015-48
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]
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|style="padding:.4em;" rowspan=2|2015/05/14
|style="padding:.4em;"|2015-47
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]
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|style="padding:.4em;"|2015-46
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]
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|style="padding:.4em;" rowspan=3|2015/05/07
|style="padding:.4em;"|2015-45
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]
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|style="padding:.4em;"|2015-44
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]
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|style="padding:.4em;"|2015-43
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]

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|style="padding:.4em;" rowspan=2|2015/04/30
|style="padding:.4em;"|2015-42
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]
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|style="padding:.4em;"|2015-41
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]
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|style="padding:.4em;" rowspan=3|2015/04/23
|style="padding:.4em;"|2015-40
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]
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|style="padding:.4em;"|2015-39
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]
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|style="padding:.4em;"|2015-38
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]
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|style="padding:.4em;" rowspan=2|2015/04/09
|style="padding:.4em;"|2015-37
|style="padding:.4em;"|
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[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]
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|style="padding:.4em;"|2015-36
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]
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|style="padding:.4em;" rowspan=2|2015/04/02
|style="padding:.4em;"|2015-35
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]
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|style="padding:.4em;"|2015-34
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]
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|style="padding:.4em;" rowspan=2|2015/03/26
|style="padding:.4em;"|2015-33
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]
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|style="padding:.4em;"|2015-32
|style="padding:.4em;"|
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[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.]
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|style="padding:.4em;" rowspan=2|2015/03/19
|style="padding:.4em;"|2015-31
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2015-30
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]
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|style="padding:.4em;" rowspan=3|2015/03/12
|style="padding:.4em;"|2015-29
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]
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|style="padding:.4em;"|2015-28
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]
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|style="padding:.4em;"|2015-27
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]
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|style="padding:.4em;" rowspan=3|2015/03/09
|style="padding:.4em;"|2015-26
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]
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|style="padding:.4em;"|2015-25
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2015-24
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]
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|style="padding:.4em;" rowspan=3|2015/03/02
|style="padding:.4em;"|2015-23
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]
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|style="padding:.4em;"|2015-22
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2015-21
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]
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|style="padding:.4em;" rowspan=3|2015/02/24
|style="padding:.4em;"|2015-20
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]
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|style="padding:.4em;"|2015-19
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]
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|style="padding:.4em;"|2015-18
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]
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|style="padding:.4em;" rowspan=3|2015/02/16
|style="padding:.4em;"|2015-17
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]
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|style="padding:.4em;"|2015-16
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]
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|style="padding:.4em;"|2015-15
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]
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|style="padding:.4em;" rowspan=4|2015/02/02
|style="padding:.4em;"|2015-14
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]
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|style="padding:.4em;"|2015-13
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]
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|style="padding:.4em;"|2015-12
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]
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|style="padding:.4em;"|2015-11
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;" rowspan=5|2015/01/26
|style="padding:.4em;"|2015-10
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]
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|style="padding:.4em;"|2015-09
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]
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|style="padding:.4em;"|2015-08
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]
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|style="padding:.4em;"|2015-07
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]
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|style="padding:.4em;"|2015-06
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]
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|style="padding:.4em;" rowspan=3|2015/01/12
|style="padding:.4em;"|2015-05
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]
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|style="padding:.4em;"|2015-04
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]
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|style="padding:.4em;"|2015-03
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]
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|style="padding:.4em;" rowspan=2|2015/01/05
|style="padding:.4em;"|2015-02
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]
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|style="padding:.4em;"|2015-01
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[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.]
|}
{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2014
|-
!scope="col" style="padding:.4em" | Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
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|style="padding:.4em;" rowspan=2|2014/12/23
|style="padding:.4em;"|2014-41
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]
|-
|style="padding:.4em;"|2014-40
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]
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|style="padding:.4em;" rowspan=4|2014/12/09
|style="padding:.4em;"|2014-39
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]
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|style="padding:.4em;"|2014-38
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]
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|style="padding:.4em;"|2014-37
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]
|-
|style="padding:.4em;"|2014-36
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]
|-
|style="padding:.4em;" rowspan=2|2014/12/02
|style="padding:.4em;"|2014-35
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]
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|style="padding:.4em;"|2014-34
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]
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|style="padding:.4em;" rowspan=2|2014/11/25
|style="padding:.4em;"|2014-33
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2014-32
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]
|-
|style="padding:.4em;" rowspan=2|2014/11/18
|style="padding:.4em;"|2014-31
|style="padding:.4em;"|SM Yang
|style="padding:.4em;text-align:left"|
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]
|-
|style="padding:.4em;"|2014-30
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]
|-
|style="padding:.4em;" rowspan=3|2014/11/11
|style="padding:.4em;"|2014-29
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]
|-
|style="padding:.4em;"|2014-28
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]
|-
|style="padding:.4em;"|2014-27
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]
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|style="padding:.4em;" rowspan=2|2014/11/04
|style="padding:.4em;"|2014-26
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]
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|style="padding:.4em;"|2014-25
|style="padding:.4em;"|JH Shin
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]
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|style="padding:.4em;" rowspan=2|2014/10/28
|style="padding:.4em;"|2014-24
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]
|-
|style="padding:.4em;"|2014-23
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[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.]
|-
|style="padding:.4em;" rowspan=2|2014/09/30
|style="padding:.4em;"|2014-22
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]
|-
|style="padding:.4em;"|2014-21
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]
|-
|style="padding:.4em;" rowspan=2|2014/09/23
|style="padding:.4em;"|2014-20
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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.]
|-
|style="padding:.4em;"|2014-19
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]
|-
|style="padding:.4em;" rowspan=2|2014/09/16
|style="padding:.4em;"|2014-18
|style="padding:.4em;"|JH Shin
|style="padding:.4em;text-align:left"|
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]
|-
|style="padding:.4em;"|2014-17
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]
|-
|style="padding:.4em;" rowspan=2|2014/09/02
|style="padding:.4em;"|2014-16
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]
|-
|style="padding:.4em;"|2014-15
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]
|-
|style="padding:.4em;" rowspan=2|2014/08/19
|style="padding:.4em;"|2014-14
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]
|-
|style="padding:.4em;"|2014-13
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]
|-
|style="padding:.4em;" rowspan=2|2014/08/12
|style="padding:.4em;"|2014-12
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]
|-
|style="padding:.4em;"|2014-11
|style="padding:.4em;"|HJ Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]
|-
|style="padding:.4em;" rowspan=2|2014/08/05
|style="padding:.4em;"|2014-10
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]
|-
|style="padding:.4em;"|2014-9
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]
|-
|style="padding:.4em;" rowspan=3|2014/07/29
|style="padding:.4em;"|2014-8
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]
|-
|style="padding:.4em;"|2014-7
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]
|-
|style="padding:.4em;"|2014-6
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]
|-
|style="padding:.4em;" rowspan=3|2014/07/22
|style="padding:.4em;"|2014-5
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]
|-
|style="padding:.4em;"|2014-4
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]
|-
|style="padding:.4em;"|2014-3
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]
|-
|style="padding:.4em;" rowspan=2|2014/07/15
|style="padding:.4em;"|2014-2
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]
|-
|style="padding:.4em;"|2014-1
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]
|}
{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2013
|-
!scope="col" style="padding:.4em" | Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
|-
|style="padding:.4em;" rowspan=2|2013/06/26
|style="padding:.4em;"|2013-31
|style="padding:.4em;"|HJ Han
|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]
|-
|style="padding:.4em;"|2013-30
|style="padding:.4em;"|YH Ko
|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]
|-
|style="padding:.4em;" rowspan=2|2013/06/04
|style="padding:.4em;"|2013-29
|style="padding:.4em;"|KS Kim
|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]
|-
|style="padding:.4em;"|2013-28
|style="padding:.4em;"|ER Kim
|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]
|-
|style="padding:.4em;" rowspan=2|2013/05/28
|style="padding:.4em;"|2013-27
|style="padding:.4em;"|YH Ko
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]
|-
|style="padding:.4em;"|2013-26
|style="padding:.4em;"|JE Shim
|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]
|-
|style="padding:.4em;" rowspan=2|2013/05/21
|style="padding:.4em;"|2013-25
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]
|-
|style="padding:.4em;"|2013-24
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]

|-
|style="padding:.4em;" rowspan=2|2013/05/14
|style="padding:.4em;"|2013-23
|style="padding:.4em;"|JE Shim
|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]

|-
|style="padding:.4em;"|2013-22
|style="padding:.4em;"|HJ Kim
|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]
|-
|style="padding:.4em;" rowspan=2|'''2013/05/07'''
|style="padding:.4em;"|2013-21
|style="padding:.4em;"|ER Kim
|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]
|-
|style="padding:.4em;"|2013-20
|style="padding:.4em;"|HS Shim
|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]
|-
|style="padding:.4em;"|2013/04/09
|style="padding:.4em;"|2013-19
|style="padding:.4em;"|HJ Kim
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]
|-
|style="padding:.4em;"|2013/04/02
|style="padding:.4em;"|2013-18
|style="padding:.4em;"|HJ Kim
|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]
|-
|style="padding:.4em;" |2013/03/12
|style="padding:.4em;"|2013-17
|style="padding:.4em;"| ER Kim
|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]
|-
|style="padding:.4em;" rowspan=1|2013/03/05
|style="padding:.4em;"|2013-16
|style="padding:.4em;"| ER Kim
|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]
|-
|style="padding:.4em;" rowspan=3|2013/02/21
|style="padding:.4em;"|2013-15
|style="padding:.4em;"| KS Kim
|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]
|-
|style="padding:.4em;"|2013-14
|style="padding:.4em;"| KS Kim
|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]
|-
|style="padding:.4em;"|2013-13
|style="padding:.4em;"| HJ Han
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]
|-
|style="padding:.4em;" rowspan=3|2013/02/15
|style="padding:.4em;"|2013-12
|style="padding:.4em;"| HJ Han
|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]
|-
|style="padding:.4em;"|2013-11
|style="padding:.4em;"| JE Shim, CY Kim
|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]
|-
|style="padding:.4em;"|2013-10
|style="padding:.4em;"|HJ Han, JH Kim
|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]
|-
|style="padding:.4em;" rowspan=3|2013/02/08
|style="padding:.4em;"|2013-09
|style="padding:.4em;"|HJ Kim
|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]
|-
|style="padding:.4em;"|2013-08
|style="padding:.4em;"|JE Shim, CY Kim
|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]
|-
|style="padding:.4em;"|2013-07
|style="padding:.4em;"|HJ Han, JH Kim
|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]
|-
|style="padding:.4em;" rowspan=3|2013/01/25
|style="padding:.4em;"|2013-06
|style="padding:.4em;"|HJ Han, '''JH Kim'''
|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]
|-
|style="padding:.4em;"|2013-05
|style="padding:.4em;"|'''ER Kim''', HS Shim
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]
|-
|style="padding:.4em;"|2013-04
|style="padding:.4em;"|'''HJ Han''', JH Kim
|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]

|-
|style="padding:.4em;" rowspan=2|2013/01/18
|style="padding:.4em;"|2013-03
|style="padding:.4em;"|KS Kim, '''TH Kim'''
|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]
|-
|style="padding:.4em;"|2013-02
|style="padding:.4em;"|'''HJ Han''', JH Kim
|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]
|-
|style="padding:.4em;" rowspan=1|2013/01/11
|style="padding:.4em;"|2013-01
|style="padding:.4em;"| '''JE Shim''', CY Kim
|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]
|}

2012
{|border ="1"
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title
|-
|rowspan = "1"|2013/01/11
|align ="center"|2012-81
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]
|-
|rowspan = "1"|2012/12/04
|align ="center"|2012-80
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]
|-
|rowspan = "2"|2012/11/20
| align="center"|2012-79
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]
|-
| align="center"|2012-78
|[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]
|-
|rowspan = "2"|2012/11/06
| align="center"|2012-77
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]
|-
| align="center"|2012-76
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes]
|-
|rowspan = "6" |2012/07/19
| align="center"|2012-75
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]
|-
| align="center"|2012-74
|[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]
|-
| align="center"|2012-73
|[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]
|-
| align="center"|2012-72
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]
|-
| align="center"|2012-71
|[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]
|-
| align="center"|2012-70
|[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]
|-
|rowspan = "8" |2012/07/16
| align="center"|2012-69
|[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]
|-
| align="center"|2012-66
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]
|-
| align="center"|2012-65
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]
|-
| align="center"|2012-64
|[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]
|-
|align="center"|2012-63
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]
|-
|align="center"|2012-62
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]
|-
|align="center"|2012-61
|[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]
|-
|align="center"|2012-60
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]
|-
|rowspan = "3" |2012/07/13
|align="center"|2012-59
|[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]
|-
| align="center"|2012-58
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]
|-
|align="center"|2012-57
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]
|-
|rowspan = "4" |2012/07/12
|align="center"|2012-56
|[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]
|-
|align="center"|2012-55
|[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]
|-
| align="center"|2012-54
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]
|-
|align="center"|2012-53
|[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]
|-
|rowspan = "6" |2012/07/09
|align="center"|2012-52
|[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]
|-
|align="center"|2012-51
|[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]
|-
| align="center"|2012-50
|[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]
|-
|align="center"|2012-49
|[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]
|-
|align="center"|2012-48
|[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]
|-
|align="center"|2012-47
|[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]
|-
|rowspan = "6" |2012/07/06
| align="center"|2012-46
|[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)]
|-
|align="center"|2012-45
|[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]
|-
|align="center"|2012-44
|[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]
|-
|align="center"|2012-43
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]
|-
| align="center"|2012-42
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]
|-
|align="center"|2012-41
|[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]
|-
|rowspan = "6" |2012/07/02
|align="center"|2012-40
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]
|-
|align="center"|2012-39
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]
|-
| align="center"|2012-38
|[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]
|-
|align="center"|2012-37
|[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]
|-
|align="center"|2012-36
|[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]
|-
|align="center"|2012-35
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]
|-
|rowspan = "3" |2012/03/05
| align="center"|2012-34
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]
|-
|align="center"|2012-33
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]
|-
|align="center"|2012-32
|[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 ]
|-
|rowspan = "7" |2012/02/27<br />2012/02/28
| align="center"|2012-31
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]
|-
|align="center"|2012-30
|[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]
|-
|align="center"|2012-29
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]
|-
|align="center"|2012-28
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]
|-
|align="center"|2012-27
|[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]
|-
|align="center"|2012-26
|[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]
|-
|align="center"|2012-25
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]
|-
|rowspan = "5" |2012/02/06
| align="center"|2012-24
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]
|-
|align="center"|2012-23
|[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]
|-
|align="center"|2012-22
|[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]
|-
|align="center"|2012-21
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]
|-
|align="center"|2012-20
|[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]
|-
|rowspan = "5" |2012/01/30
|align="center"|2012-19
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]
|-
|align="center"|2012-18
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]
|-
|align="center"|2012-17
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]
|-
|align="center"|2012-16
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]
|-
|align="center"|2012-15
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]
|-
|rowspan = "3" |2012/01/09
|align="center"|2012-14
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]
|-
|align="center"|2012-13
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]
|-
|align="center"|2012-12
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]
|-
|rowspan = "6" |2012/01/09<br />2012/01/16
| align="center"|2012-11
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]
|-
|align="center"|2012-10
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]
|-
|align="center"|2012-09
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]
|-
|align="center"|2012-08
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]
|-
|align="center"|2012-07
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]
|-
|align="center"|2012-06
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]
|-
|rowspan = "3" |2012/01/09<br />2012/01/16
|align="center"|2012-05
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]
|-
|align="center"|2012-04
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]
|-
|align="center"|2012-03
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]
|-
|rowspan = "2" |2012/01/09<br />2012/01/16
|align="center"|2012-02
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]
|-
|align="center"|2012-01
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]
|}
2011
{|border ="1"
|style="color:black; background-color:#dcdcdc;" align="center" |Date
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title
|-
|rowspan = "6" |2011/11/28
|align="center"|2011-49
|[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]
|-
|align="center"|2011-48
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]
|-
|align="center"|2011-47
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]
|-
|align="center"|2011-46
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]
|-
|align="center"|2011-45
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]
|-
|align="center"|2011-44
|[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]
|-
|rowspan = "3" |2011/11/14
|align="center"|2011-43
|[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]
|-
|align="center"|2011-42
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]
|-
|align="center"|2011-41
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]
|-
|rowspan = "4" |2011/11/07
|align="center"|2011-40
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]
|-
|align="center"|2011-39
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]
|-
|align="center"|2011-38
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]
|-
|align="center"|2011-37
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]
|-
|rowspan = "3" |2011/11/07
|align="center"|2011-36
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]
|-
|align="center"|2011-35
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]
|-
|align="center"|2011-34
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]
|-
|rowspan = "3" |2011/10/05
|align="center"|2011-33
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]
|-
|align="center"|2011-32
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]
|-
|align="center"|2011-31
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]
|-
|rowspan = "4" |2011/10/04
|align="center"|2011-30
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]
|-
|align="center"|2011-29
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]
|-
|align="center"|2011-28
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]
|-
|align="center"|2011-27
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]
|-
|rowspan = "2" |2011/09/19
|align="center"|2011-26
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]
|-
|align="center"|2011-25
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]
|-
|rowspan = "2" |2011/09/05
|align="center"|2011-24
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]
|-
|align="center"|2011-23
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]
|-
|rowspan = "2" |2011/09/22
|align="center"|2011-22
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]
|-
|align="center"|2011-21
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]
|-
|2011/06/20
|align="center"|2011-20
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]
|-
|rowspan = "2" |2011/03/30
|align="center"|2011-19
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]
|-
|align="center"|2011-18
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]
|-
|rowspan = "2" |2011/03/16
|align="center"|2011-17
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']
|-
|align="center"|2011-16
|[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]
|-
|rowspan = "3" |2011/04/25
|align="center"|2011-15
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]
|-
|align="center"|2011-14
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]
|-
|align="center"|2011-13
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]
|-
|rowspan = "2" |2011/04/11
|align="center"|2011-12
|[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]
|-
|align="center"|2011-11
|***Changed!***
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]
|-
|rowspan = "2"|2011/03/28
|align="center"|2011-10
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]
|-
|align="center"|2011-09
|[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"|2011/03/14
|align="center"|2011-08
|[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]
|-
|align="center"|2011-07
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]
|-
|rowspan = "2"|2011/02/28
|align="center"|2011-06
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]
|-
|align="center"|2011-05
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]
|-
|2011/02/21
|align="center"|2011-04
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]
|-
|2011/02/14
|align="center"|2011-03
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]
|-
|rowspan = "2"|2011/01/31
|align="center"|2011-02
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]
|-
|align="center"|2011-01
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]
|}
2010
{|border ="1"
|style="color:black; background-color:#dcdcdc;" align="center" |Date
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title
|-
|rowspan = "2"|2010/12/27
|align="center"|2010-29
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]
|-
|align="center"|2010-28
|[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"|2010/11/15
|align="center"|2010-27
|[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]
|-
|align="center"|2010-26
|[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"|2010/11/01
|align="center"|2010-25
|[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]
|-
|align="center"|2010-24
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]
|-
|2010/10/11
|align="center"|2010-23
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]
|-
|rowspan = "2"|2010/09/13
|align="center"|2010-22
|[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]
|-
|align="center"|2010-21
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]
|-
|2010/05/26
|align="center"|2010-20
|[[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]]
|-
|2010/05/19
|align="center"|2010-19
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]
|-
|2010/04/21
|align="center"|2010-18
|[[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]]
|-
|2010/04/14
|align="center"|2010-17
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]
|-
|rowspan = "2" |2010/04/07
|align="center"|2010-16
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]
|-
|align="center"|2010-15
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]
|-
|rowspan="2"|2010/03/31
|align="center"|2010-14
|[[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]]
|-
|align="center"|2010-13
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]
|-
|2010/03/24
|align="center"|2010-12
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]
|-
|2010/01/18
|align="center"|2010-11
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies
|-
|2010/01/16
|align="center"|2010-10
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells
|-
|2010/01/15
|align="center"|2010-09
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions
|-
|2010/01/14
|align="center"|2010-08
|chemogenomic_profiling_predicts_antifungal_synergies
|-
|2010/01/13
|align="center"|2010-07
|edgetic_perturbation_models_of_human_inherited_disorders
|-
|2010/01/12
|align="center"|2010-06
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans
|-
|2010/01/11
|align="center"|2010-05
|predicting_new_molecular_targets_for_known_drugs.pdf
Reference:SEA(Similarity Ensemble Approach)
|-
|2010/01/09
|align="center"|2010-04
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance
|-
|2010/01/08
|align="center"|2010-03
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer
|-
|2010/01/07
|align="center"|2010-02
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network
|-
|2010/01/06
|align="center"|2010-01
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs
|}

Journal Club

2018-05-07T06:10:54Z

Dreadcupper:

{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2018
|-
!scope="col" style="padding:.4em" |Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
|-
|style="padding:.4em;" rowspan=2|2018/06/14
|style="padding:.4em;"|18-12
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=A+pan-cancer+analysis+of+enhancer+expression+in+nearly+9000+patient+samples A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.]
|-
|style="padding:.4em;"|18-11
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Machine+learning+identifies+stemness+features+associated+with+oncogenic+dedifferentiation Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.]
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|style="padding:.4em;" rowspan=2|2018/06/07
|style="padding:.4em;"|18-10
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[hhttps://www.ncbi.nlm.nih.gov/pubmed/?term=Developmental+and+oncogenic+programs+in+H3K27M+gliomas+dissected+by+single-cell+RNA-seq Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq.]
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|style="padding:.4em;"|18-9
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Chemoresistance+evolution+in+triple-negative+breast+cancer+delineated+by+single-cell+sequencing Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing.]
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|style="padding:.4em;" rowspan=2|2018/05/31
|style="padding:.4em;"|18-8
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Mapping+human+pluripotent+stem+cell+differentiation+pathways+using+high+throughput+single-cell+RNA-sequencing Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing.]
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|style="padding:.4em;"|18-7
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=A+single-cell+RNA-seq+survey+of+the+developmental+landscape+of+the+human+prefrontal+cortex A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex.]
|-
|style="padding:.4em;" rowspan=2|2018/05/24
|style="padding:.4em;"|18-6
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Single-cell+RNA+sequencing+identifies+celltype-specific+cis-eQTLs+and+co-expression+QTLs Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs.]
|-
|style="padding:.4em;"|18-5
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=FOCS%3A+a+novel+method+for+analyzing+enhancer+and+gene+activity+patterns+infers+an+extensive+enhancer-promoter+map FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map.]
|-
|style="padding:.4em;" rowspan=2|2018/05/17
|style="padding:.4em;"|18-4
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/29149608 A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.]
|-
|style="padding:.4em;"|18-3
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/29610481 A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.]
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|style="padding:.4em;" rowspan=2|2018/05/20
|style="padding:.4em;"|18-2
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Inferring+regulatory+element+landscapes+and+transcription+factor+networks+from+cancer+methylomes Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.]
|-
|style="padding:.4em;"|18-1
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/28129544 Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma.]
|}
{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2017
|-
!scope="col" style="padding:.4em" |Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
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|style="padding:.4em;" rowspan=2|2017/06/28
|style="padding:.4em;"|17-36
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/28104840 Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy.]
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|style="padding:.4em;"|17-35
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27240091 Landscape of tumor-infiltrating T cell repertoire of human cancers.]
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|style="padding:.4em;" rowspan=2|2017/06/14
|style="padding:.4em;"|17-34
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2015/09/01/025908 The landscape of T cell infiltration in human cancer and its association with antigen presenting gene expression.]
|-
|style="padding:.4em;"|17-33
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.08.052 A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.]
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|style="padding:.4em;" rowspan=2|2017/06/07
|style="padding:.4em;"|17-32
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.tandfonline.com/doi/full/10.1080/2162402X.2016.1253654 Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis.]
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|style="padding:.4em;"|17-31
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.celrep.2016.03.075 Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.]
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|style="padding:.4em;" rowspan=2|2017/05/31
|style="padding:.4em;"|17-30
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.02.065 Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma.]
|-
|style="padding:.4em;"|17-29
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.celrep.2016.12.019 Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade.]
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|style="padding:.4em;" rowspan=2|2017/05/24
|style="padding:.4em;"|17-28
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.12.022 Systemic Immunity Is Required for Effective Cencer Immunotherapy.]
|-
|style="padding:.4em;"|17-27
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.10.020 Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.]
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|style="padding:.4em;" rowspan=2|2017/05/17
|style="padding:.4em;"|17-26
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.10.018 Host and Environmental Factors Influencing Individual Human Cytokine Responses.]
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|style="padding:.4em;"|17-25
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.10.017 A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans.]
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|style="padding:.4em;" rowspan=2|2017/04/26
|style="padding:.4em;"|17-24
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1038%2FNMETH.4177 Pooled CRISPR screening with single-cell transcriptome readout.]
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|style="padding:.4em;"|17-23
|style="padding:.4em;"|
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[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.11.039 Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq.]
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|style="padding:.4em;" rowspan=2|2017/04/12
|style="padding:.4em;"|17-22
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.11.038 Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.]
|-
|style="padding:.4em;"|17-21
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1038%2Fnbt.3569 Wishbone identifies bifurcating developmental trajectories from single-cell data.]
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|style="padding:.4em;" rowspan=2|2017/04/05
|style="padding:.4em;"|17-20
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2017/02/21/110668 Reversed graph embedding resolves complex single-cell developmental trajectories.]
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|style="padding:.4em;"|17-19
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1038%2Fnmeth.4150 Single-cell mRNA quantification and differential analysis with Census.]
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|style="padding:.4em;" rowspan=2|2017/03/29
|style="padding:.4em;"|17-18
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[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.celrep.2016.12.060 Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage.]
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|style="padding:.4em;"|17-17
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/26051941 Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis.]
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|style="padding:.4em;" rowspan=2|2017/03/22
|style="padding:.4em;"|17-16
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[https://www.ncbi.nlm.nih.gov/pubmed/27580035 Single-cell analysis of mixed-lineage states leading to a binary cell fate choice.]
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|style="padding:.4em;"|17-15
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27281220 Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq.]
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|style="padding:.4em;" rowspan=2|2017/03/15
|style="padding:.4em;"|17-14
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[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1126%2Fscience.aad0501 Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.]
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|style="padding:.4em;"|17-13
|style="padding:.4em;"|
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[https://www.ncbi.nlm.nih.gov/pubmed/26084335 Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells.]
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|style="padding:.4em;" rowspan=2|2017/02/28
|style="padding:.4em;"|17-12
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27824113 A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions.]
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|style="padding:.4em;"|17-11
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[//pubmed.gov/27851969 Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types.]
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|style="padding:.4em;" rowspan=2|2017/02/21
|style="padding:.4em;"|17-10
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2016/12/30/097451 Convergence of dispersed regulatory mutations predicts driver genes in prostate cancer.]
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|style="padding:.4em;"|17-09
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[//pubmed.gov/27723759 Chromatin structure-based prediction of recurrent noncoding mutations in cancer.]
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|style="padding:.4em;" rowspan=2|2017/02/07
|style="padding:.4em;"|17-08
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2016/11/17/088286 Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade.]
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|style="padding:.4em;"|17-07
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2016/11/28/090134 Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer.]
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|style="padding:.4em;" rowspan=1|2017/01/31
|style="padding:.4em;"|17-06
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/27912059 Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations.]
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|style="padding:.4em;" rowspan=1|2017/01/24
|style="padding:.4em;"|17-05
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/27851914 Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells.]
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|style="padding:.4em;" rowspan=2|2017/01/17
|style="padding:.4em;"|17-04
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/25938943 Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C]
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|style="padding:.4em;"|17-03
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/27306882 CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.]
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|style="padding:.4em;" rowspan=1|2017/01/10
|style="padding:.4em;"|17-02
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/26527291 ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis]
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|style="padding:.4em;" rowspan=1|2017/01/03
|style="padding:.4em;"|17-01
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/26287467 Single-cell messenger RNA sequencing reveals rare intestinal cell types]
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{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2016
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!scope="col" style="padding:.4em" |Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
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|style="padding:.4em;" rowspan=1|2016/12/27
|style="padding:.4em;"|2016-31
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/25664528 Decoding the regulatory network of early blood development from single-cell gene expression measurements.]
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|style="padding:.4em;" rowspan=1|2016/12/6
|style="padding:.4em;"|2016-30
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26299571 Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.]
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|style="padding:.4em;" rowspan=1|2016/11/29
|style="padding:.4em;"|2016-29
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/24658644 The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.]
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|style="padding:.4em;" rowspan=1|2016/11/22
|style="padding:.4em;"|2016-28
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26887813 Classification of low quality cells from single-cell RNA-seq data.]
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|style="padding:.4em;" rowspan=1|2016/11/15
|style="padding:.4em;"|2016-27
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26000487 Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.]
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|style="padding:.4em;" rowspan=1|2016/11/8
|style="padding:.4em;"|2016-26
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26000488 Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.]
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|style="padding:.4em;" rowspan=1|2016/11/1
|style="padding:.4em;"|2016-25
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27426982 Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.]
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|style="padding:.4em;" rowspan=1|2016/10/25
|style="padding:.4em;"|2016-24
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27549193 Comprehensive analyses of tumor immunity: implications for cancer immunotherapy.]
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|style="padding:.4em;" rowspan=1|2016/10/11
|style="padding:.4em;"|2016-23
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=sidespread+parainflammation Widespread parainflammation in human cancer]
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|style="padding:.4em;" rowspan=1|2016/9/27
|style="padding:.4em;"|2016-22
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27535533 Analysis of protein-coding genetic variation in 60,706 humans]
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|style="padding:.4em;" rowspan=1|2016/9/20
|style="padding:.4em;"|2016-21
|style="padding:.4em;"|SM Yang
|style="padding:.4em;text-align:left"|
Functional characterization of somatic mutations in cancer using network-based inference of protein activity
[http://www.ncbi.nlm.nih.gov/pubmed/27322546 pubmed]
[http://www.nature.com/ng/journal/v48/n8/full/ng.3593.html fulltext]
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|style="padding:.4em;" rowspan=1|2016/9/13
|style="padding:.4em;"|2016-20
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=exploiting+single-cell+expression+to+characterize Exploiting single-cell expression to characterize co-expression replicability.]
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|style="padding:.4em;" rowspan=1|2016/9/6
|style="padding:.4em;"|2016-19
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26940869 Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade]
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|style="padding:.4em;" rowspan=1|2016/8/31
|style="padding:.4em;"|2016-18
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27264179 A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors]
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|style="padding:.4em;" rowspan=1|2016/8/16
|style="padding:.4em;"|2016-17
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27309802 The landscape of accessible chromatin in mammalian preimplantation embryos]
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|style="padding:.4em;" rowspan=1|2016/8/8
|style="padding:.4em;"|2016-16
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27064255 Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin]
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|style="padding:.4em;" rowspan=1|2016/8/1
|style="padding:.4em;"|2016-15
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27040498 Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients]
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|style="padding:.4em;" rowspan=1|2016/7/25
|style="padding:.4em;"|2016-14
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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]
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|style="padding:.4em;" rowspan=1|2016/7/18
|style="padding:.4em;"|2016-13
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]
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|style="padding:.4em;" rowspan=2|2016/6/8
|style="padding:.4em;"|2016-12
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]
|-
|style="padding:.4em;"| 2016-11
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]
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|style="padding:.4em;" rowspan=2|2016/6/1
|style="padding:.4em;"|2016-10
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]
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|style="padding:.4em;"| 2016-9
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]
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|style="padding:.4em;" rowspan=2|2016/5/18
|style="padding:.4em;"|2016-8
|style="padding:.4em;"|CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]
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|style="padding:.4em;"| 2016-7
|style="padding:.4em;"| CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]
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|style="padding:.4em;" rowspan=2|2016/5/11
|style="padding:.4em;"|2016-6
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]
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|style="padding:.4em;"| 2016-5
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]
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|style="padding:.4em;" rowspan=2|2016/5/4
|style="padding:.4em;"|2016-4
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[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]
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|style="padding:.4em;"| 2016-3
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]
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|style="padding:.4em;" rowspan=2|2016/4/27
|style="padding:.4em;"|2016-2
|style="padding:.4em;"|CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]
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|style="padding:.4em;"| 2016-1
|style="padding:.4em;"| CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]
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{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2015
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!scope="col" style="padding:.4em" | Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
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|style="padding:.4em;" rowspan=2|2015/06/11
|style="padding:.4em;"|2015-55
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]
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|style="padding:.4em;"|2015-54
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;" rowspan=2|2015/06/04
|style="padding:.4em;"|2015-53
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]
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|style="padding:.4em;"|2015-52
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]
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|style="padding:.4em;" rowspan=2|2015/05/28
|style="padding:.4em;"|2015-51
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2015-50
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]
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|style="padding:.4em;" rowspan=2|2015/05/21
|style="padding:.4em;"|2015-49
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]
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|style="padding:.4em;"|2015-48
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]
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|style="padding:.4em;" rowspan=2|2015/05/14
|style="padding:.4em;"|2015-47
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]
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|style="padding:.4em;"|2015-46
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]
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|style="padding:.4em;" rowspan=3|2015/05/07
|style="padding:.4em;"|2015-45
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]
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|style="padding:.4em;"|2015-44
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]
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|style="padding:.4em;"|2015-43
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]

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|style="padding:.4em;" rowspan=2|2015/04/30
|style="padding:.4em;"|2015-42
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]
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|style="padding:.4em;"|2015-41
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]
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|style="padding:.4em;" rowspan=3|2015/04/23
|style="padding:.4em;"|2015-40
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]
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|style="padding:.4em;"|2015-39
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]
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|style="padding:.4em;"|2015-38
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]
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|style="padding:.4em;" rowspan=2|2015/04/09
|style="padding:.4em;"|2015-37
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]
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|style="padding:.4em;"|2015-36
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]
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|style="padding:.4em;" rowspan=2|2015/04/02
|style="padding:.4em;"|2015-35
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]
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|style="padding:.4em;"|2015-34
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]
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|style="padding:.4em;" rowspan=2|2015/03/26
|style="padding:.4em;"|2015-33
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]
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|style="padding:.4em;"|2015-32
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;" rowspan=2|2015/03/19
|style="padding:.4em;"|2015-31
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2015-30
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]
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|style="padding:.4em;" rowspan=3|2015/03/12
|style="padding:.4em;"|2015-29
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]
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|style="padding:.4em;"|2015-28
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]
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|style="padding:.4em;"|2015-27
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]
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|style="padding:.4em;" rowspan=3|2015/03/09
|style="padding:.4em;"|2015-26
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]
|-
|style="padding:.4em;"|2015-25
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|
[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.]
|-
|style="padding:.4em;"|2015-24
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]
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|style="padding:.4em;" rowspan=3|2015/03/02
|style="padding:.4em;"|2015-23
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]
|-
|style="padding:.4em;"|2015-22
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2015-21
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]
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|style="padding:.4em;" rowspan=3|2015/02/24
|style="padding:.4em;"|2015-20
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]
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|style="padding:.4em;"|2015-19
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]
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|style="padding:.4em;"|2015-18
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]
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|style="padding:.4em;" rowspan=3|2015/02/16
|style="padding:.4em;"|2015-17
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]
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|style="padding:.4em;"|2015-16
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]
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|style="padding:.4em;"|2015-15
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]
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|style="padding:.4em;" rowspan=4|2015/02/02
|style="padding:.4em;"|2015-14
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]
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|style="padding:.4em;"|2015-13
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]
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|style="padding:.4em;"|2015-12
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]
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|style="padding:.4em;"|2015-11
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;" rowspan=5|2015/01/26
|style="padding:.4em;"|2015-10
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]
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|style="padding:.4em;"|2015-09
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]
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|style="padding:.4em;"|2015-08
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]
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|style="padding:.4em;"|2015-07
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]
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|style="padding:.4em;"|2015-06
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]
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|style="padding:.4em;" rowspan=3|2015/01/12
|style="padding:.4em;"|2015-05
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]
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|style="padding:.4em;"|2015-04
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]
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|style="padding:.4em;"|2015-03
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]
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|style="padding:.4em;" rowspan=2|2015/01/05
|style="padding:.4em;"|2015-02
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]
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|style="padding:.4em;"|2015-01
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[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.]
|}
{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2014
|-
!scope="col" style="padding:.4em" | Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
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|style="padding:.4em;" rowspan=2|2014/12/23
|style="padding:.4em;"|2014-41
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]
|-
|style="padding:.4em;"|2014-40
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]
|-
|style="padding:.4em;" rowspan=4|2014/12/09
|style="padding:.4em;"|2014-39
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]
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|style="padding:.4em;"|2014-38
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]
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|style="padding:.4em;"|2014-37
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]
|-
|style="padding:.4em;"|2014-36
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]
|-
|style="padding:.4em;" rowspan=2|2014/12/02
|style="padding:.4em;"|2014-35
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]
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|style="padding:.4em;"|2014-34
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]
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|style="padding:.4em;" rowspan=2|2014/11/25
|style="padding:.4em;"|2014-33
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2014-32
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]
|-
|style="padding:.4em;" rowspan=2|2014/11/18
|style="padding:.4em;"|2014-31
|style="padding:.4em;"|SM Yang
|style="padding:.4em;text-align:left"|
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]
|-
|style="padding:.4em;"|2014-30
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]
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|style="padding:.4em;" rowspan=3|2014/11/11
|style="padding:.4em;"|2014-29
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]
|-
|style="padding:.4em;"|2014-28
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]
|-
|style="padding:.4em;"|2014-27
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]
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|style="padding:.4em;" rowspan=2|2014/11/04
|style="padding:.4em;"|2014-26
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]
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|style="padding:.4em;"|2014-25
|style="padding:.4em;"|JH Shin
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]
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|style="padding:.4em;" rowspan=2|2014/10/28
|style="padding:.4em;"|2014-24
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]
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|style="padding:.4em;"|2014-23
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;" rowspan=2|2014/09/30
|style="padding:.4em;"|2014-22
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]
|-
|style="padding:.4em;"|2014-21
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]
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|style="padding:.4em;" rowspan=2|2014/09/23
|style="padding:.4em;"|2014-20
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2014-19
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]
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|style="padding:.4em;" rowspan=2|2014/09/16
|style="padding:.4em;"|2014-18
|style="padding:.4em;"|JH Shin
|style="padding:.4em;text-align:left"|
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]
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|style="padding:.4em;"|2014-17
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]
|-
|style="padding:.4em;" rowspan=2|2014/09/02
|style="padding:.4em;"|2014-16
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]
|-
|style="padding:.4em;"|2014-15
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]
|-
|style="padding:.4em;" rowspan=2|2014/08/19
|style="padding:.4em;"|2014-14
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]
|-
|style="padding:.4em;"|2014-13
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]
|-
|style="padding:.4em;" rowspan=2|2014/08/12
|style="padding:.4em;"|2014-12
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]
|-
|style="padding:.4em;"|2014-11
|style="padding:.4em;"|HJ Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]
|-
|style="padding:.4em;" rowspan=2|2014/08/05
|style="padding:.4em;"|2014-10
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]
|-
|style="padding:.4em;"|2014-9
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]
|-
|style="padding:.4em;" rowspan=3|2014/07/29
|style="padding:.4em;"|2014-8
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]
|-
|style="padding:.4em;"|2014-7
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]
|-
|style="padding:.4em;"|2014-6
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]
|-
|style="padding:.4em;" rowspan=3|2014/07/22
|style="padding:.4em;"|2014-5
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]
|-
|style="padding:.4em;"|2014-4
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]
|-
|style="padding:.4em;"|2014-3
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]
|-
|style="padding:.4em;" rowspan=2|2014/07/15
|style="padding:.4em;"|2014-2
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]
|-
|style="padding:.4em;"|2014-1
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]
|}
{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2013
|-
!scope="col" style="padding:.4em" | Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
|-
|style="padding:.4em;" rowspan=2|2013/06/26
|style="padding:.4em;"|2013-31
|style="padding:.4em;"|HJ Han
|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]
|-
|style="padding:.4em;"|2013-30
|style="padding:.4em;"|YH Ko
|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]
|-
|style="padding:.4em;" rowspan=2|2013/06/04
|style="padding:.4em;"|2013-29
|style="padding:.4em;"|KS Kim
|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]
|-
|style="padding:.4em;"|2013-28
|style="padding:.4em;"|ER Kim
|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]
|-
|style="padding:.4em;" rowspan=2|2013/05/28
|style="padding:.4em;"|2013-27
|style="padding:.4em;"|YH Ko
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]
|-
|style="padding:.4em;"|2013-26
|style="padding:.4em;"|JE Shim
|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]
|-
|style="padding:.4em;" rowspan=2|2013/05/21
|style="padding:.4em;"|2013-25
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]
|-
|style="padding:.4em;"|2013-24
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]

|-
|style="padding:.4em;" rowspan=2|2013/05/14
|style="padding:.4em;"|2013-23
|style="padding:.4em;"|JE Shim
|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]

|-
|style="padding:.4em;"|2013-22
|style="padding:.4em;"|HJ Kim
|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]
|-
|style="padding:.4em;" rowspan=2|'''2013/05/07'''
|style="padding:.4em;"|2013-21
|style="padding:.4em;"|ER Kim
|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]
|-
|style="padding:.4em;"|2013-20
|style="padding:.4em;"|HS Shim
|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]
|-
|style="padding:.4em;"|2013/04/09
|style="padding:.4em;"|2013-19
|style="padding:.4em;"|HJ Kim
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]
|-
|style="padding:.4em;"|2013/04/02
|style="padding:.4em;"|2013-18
|style="padding:.4em;"|HJ Kim
|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]
|-
|style="padding:.4em;" |2013/03/12
|style="padding:.4em;"|2013-17
|style="padding:.4em;"| ER Kim
|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]
|-
|style="padding:.4em;" rowspan=1|2013/03/05
|style="padding:.4em;"|2013-16
|style="padding:.4em;"| ER Kim
|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]
|-
|style="padding:.4em;" rowspan=3|2013/02/21
|style="padding:.4em;"|2013-15
|style="padding:.4em;"| KS Kim
|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]
|-
|style="padding:.4em;"|2013-14
|style="padding:.4em;"| KS Kim
|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]
|-
|style="padding:.4em;"|2013-13
|style="padding:.4em;"| HJ Han
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]
|-
|style="padding:.4em;" rowspan=3|2013/02/15
|style="padding:.4em;"|2013-12
|style="padding:.4em;"| HJ Han
|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]
|-
|style="padding:.4em;"|2013-11
|style="padding:.4em;"| JE Shim, CY Kim
|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]
|-
|style="padding:.4em;"|2013-10
|style="padding:.4em;"|HJ Han, JH Kim
|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]
|-
|style="padding:.4em;" rowspan=3|2013/02/08
|style="padding:.4em;"|2013-09
|style="padding:.4em;"|HJ Kim
|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]
|-
|style="padding:.4em;"|2013-08
|style="padding:.4em;"|JE Shim, CY Kim
|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]
|-
|style="padding:.4em;"|2013-07
|style="padding:.4em;"|HJ Han, JH Kim
|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]
|-
|style="padding:.4em;" rowspan=3|2013/01/25
|style="padding:.4em;"|2013-06
|style="padding:.4em;"|HJ Han, '''JH Kim'''
|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]
|-
|style="padding:.4em;"|2013-05
|style="padding:.4em;"|'''ER Kim''', HS Shim
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]
|-
|style="padding:.4em;"|2013-04
|style="padding:.4em;"|'''HJ Han''', JH Kim
|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]

|-
|style="padding:.4em;" rowspan=2|2013/01/18
|style="padding:.4em;"|2013-03
|style="padding:.4em;"|KS Kim, '''TH Kim'''
|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]
|-
|style="padding:.4em;"|2013-02
|style="padding:.4em;"|'''HJ Han''', JH Kim
|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]
|-
|style="padding:.4em;" rowspan=1|2013/01/11
|style="padding:.4em;"|2013-01
|style="padding:.4em;"| '''JE Shim''', CY Kim
|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]
|}

2012
{|border ="1"
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title
|-
|rowspan = "1"|2013/01/11
|align ="center"|2012-81
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]
|-
|rowspan = "1"|2012/12/04
|align ="center"|2012-80
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]
|-
|rowspan = "2"|2012/11/20
| align="center"|2012-79
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]
|-
| align="center"|2012-78
|[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]
|-
|rowspan = "2"|2012/11/06
| align="center"|2012-77
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]
|-
| align="center"|2012-76
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes]
|-
|rowspan = "6" |2012/07/19
| align="center"|2012-75
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]
|-
| align="center"|2012-74
|[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]
|-
| align="center"|2012-73
|[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]
|-
| align="center"|2012-72
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]
|-
| align="center"|2012-71
|[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]
|-
| align="center"|2012-70
|[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]
|-
|rowspan = "8" |2012/07/16
| align="center"|2012-69
|[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]
|-
| align="center"|2012-66
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]
|-
| align="center"|2012-65
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]
|-
| align="center"|2012-64
|[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]
|-
|align="center"|2012-63
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]
|-
|align="center"|2012-62
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]
|-
|align="center"|2012-61
|[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]
|-
|align="center"|2012-60
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]
|-
|rowspan = "3" |2012/07/13
|align="center"|2012-59
|[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]
|-
| align="center"|2012-58
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]
|-
|align="center"|2012-57
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]
|-
|rowspan = "4" |2012/07/12
|align="center"|2012-56
|[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]
|-
|align="center"|2012-55
|[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]
|-
| align="center"|2012-54
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]
|-
|align="center"|2012-53
|[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]
|-
|rowspan = "6" |2012/07/09
|align="center"|2012-52
|[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]
|-
|align="center"|2012-51
|[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]
|-
| align="center"|2012-50
|[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]
|-
|align="center"|2012-49
|[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]
|-
|align="center"|2012-48
|[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]
|-
|align="center"|2012-47
|[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]
|-
|rowspan = "6" |2012/07/06
| align="center"|2012-46
|[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)]
|-
|align="center"|2012-45
|[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]
|-
|align="center"|2012-44
|[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]
|-
|align="center"|2012-43
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]
|-
| align="center"|2012-42
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]
|-
|align="center"|2012-41
|[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]
|-
|rowspan = "6" |2012/07/02
|align="center"|2012-40
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]
|-
|align="center"|2012-39
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]
|-
| align="center"|2012-38
|[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]
|-
|align="center"|2012-37
|[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]
|-
|align="center"|2012-36
|[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]
|-
|align="center"|2012-35
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]
|-
|rowspan = "3" |2012/03/05
| align="center"|2012-34
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]
|-
|align="center"|2012-33
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]
|-
|align="center"|2012-32
|[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 ]
|-
|rowspan = "7" |2012/02/27<br />2012/02/28
| align="center"|2012-31
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]
|-
|align="center"|2012-30
|[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]
|-
|align="center"|2012-29
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]
|-
|align="center"|2012-28
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]
|-
|align="center"|2012-27
|[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]
|-
|align="center"|2012-26
|[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]
|-
|align="center"|2012-25
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]
|-
|rowspan = "5" |2012/02/06
| align="center"|2012-24
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]
|-
|align="center"|2012-23
|[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]
|-
|align="center"|2012-22
|[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]
|-
|align="center"|2012-21
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]
|-
|align="center"|2012-20
|[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]
|-
|rowspan = "5" |2012/01/30
|align="center"|2012-19
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]
|-
|align="center"|2012-18
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]
|-
|align="center"|2012-17
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]
|-
|align="center"|2012-16
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]
|-
|align="center"|2012-15
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]
|-
|rowspan = "3" |2012/01/09
|align="center"|2012-14
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]
|-
|align="center"|2012-13
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]
|-
|align="center"|2012-12
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]
|-
|rowspan = "6" |2012/01/09<br />2012/01/16
| align="center"|2012-11
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]
|-
|align="center"|2012-10
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]
|-
|align="center"|2012-09
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]
|-
|align="center"|2012-08
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]
|-
|align="center"|2012-07
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]
|-
|align="center"|2012-06
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]
|-
|rowspan = "3" |2012/01/09<br />2012/01/16
|align="center"|2012-05
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]
|-
|align="center"|2012-04
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]
|-
|align="center"|2012-03
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]
|-
|rowspan = "2" |2012/01/09<br />2012/01/16
|align="center"|2012-02
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]
|-
|align="center"|2012-01
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]
|}
2011
{|border ="1"
|style="color:black; background-color:#dcdcdc;" align="center" |Date
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title
|-
|rowspan = "6" |2011/11/28
|align="center"|2011-49
|[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]
|-
|align="center"|2011-48
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]
|-
|align="center"|2011-47
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]
|-
|align="center"|2011-46
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]
|-
|align="center"|2011-45
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]
|-
|align="center"|2011-44
|[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]
|-
|rowspan = "3" |2011/11/14
|align="center"|2011-43
|[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]
|-
|align="center"|2011-42
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]
|-
|align="center"|2011-41
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]
|-
|rowspan = "4" |2011/11/07
|align="center"|2011-40
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]
|-
|align="center"|2011-39
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]
|-
|align="center"|2011-38
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]
|-
|align="center"|2011-37
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]
|-
|rowspan = "3" |2011/11/07
|align="center"|2011-36
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]
|-
|align="center"|2011-35
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]
|-
|align="center"|2011-34
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]
|-
|rowspan = "3" |2011/10/05
|align="center"|2011-33
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]
|-
|align="center"|2011-32
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]
|-
|align="center"|2011-31
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]
|-
|rowspan = "4" |2011/10/04
|align="center"|2011-30
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]
|-
|align="center"|2011-29
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]
|-
|align="center"|2011-28
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]
|-
|align="center"|2011-27
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]
|-
|rowspan = "2" |2011/09/19
|align="center"|2011-26
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]
|-
|align="center"|2011-25
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]
|-
|rowspan = "2" |2011/09/05
|align="center"|2011-24
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]
|-
|align="center"|2011-23
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]
|-
|rowspan = "2" |2011/09/22
|align="center"|2011-22
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]
|-
|align="center"|2011-21
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]
|-
|2011/06/20
|align="center"|2011-20
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]
|-
|rowspan = "2" |2011/03/30
|align="center"|2011-19
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]
|-
|align="center"|2011-18
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]
|-
|rowspan = "2" |2011/03/16
|align="center"|2011-17
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']
|-
|align="center"|2011-16
|[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]
|-
|rowspan = "3" |2011/04/25
|align="center"|2011-15
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]
|-
|align="center"|2011-14
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]
|-
|align="center"|2011-13
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]
|-
|rowspan = "2" |2011/04/11
|align="center"|2011-12
|[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]
|-
|align="center"|2011-11
|***Changed!***
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]
|-
|rowspan = "2"|2011/03/28
|align="center"|2011-10
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]
|-
|align="center"|2011-09
|[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"|2011/03/14
|align="center"|2011-08
|[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]
|-
|align="center"|2011-07
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]
|-
|rowspan = "2"|2011/02/28
|align="center"|2011-06
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]
|-
|align="center"|2011-05
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]
|-
|2011/02/21
|align="center"|2011-04
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]
|-
|2011/02/14
|align="center"|2011-03
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]
|-
|rowspan = "2"|2011/01/31
|align="center"|2011-02
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]
|-
|align="center"|2011-01
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]
|}
2010
{|border ="1"
|style="color:black; background-color:#dcdcdc;" align="center" |Date
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title
|-
|rowspan = "2"|2010/12/27
|align="center"|2010-29
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]
|-
|align="center"|2010-28
|[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"|2010/11/15
|align="center"|2010-27
|[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]
|-
|align="center"|2010-26
|[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"|2010/11/01
|align="center"|2010-25
|[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]
|-
|align="center"|2010-24
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]
|-
|2010/10/11
|align="center"|2010-23
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]
|-
|rowspan = "2"|2010/09/13
|align="center"|2010-22
|[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]
|-
|align="center"|2010-21
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]
|-
|2010/05/26
|align="center"|2010-20
|[[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]]
|-
|2010/05/19
|align="center"|2010-19
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]
|-
|2010/04/21
|align="center"|2010-18
|[[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]]
|-
|2010/04/14
|align="center"|2010-17
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]
|-
|rowspan = "2" |2010/04/07
|align="center"|2010-16
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]
|-
|align="center"|2010-15
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]
|-
|rowspan="2"|2010/03/31
|align="center"|2010-14
|[[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]]
|-
|align="center"|2010-13
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]
|-
|2010/03/24
|align="center"|2010-12
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]
|-
|2010/01/18
|align="center"|2010-11
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies
|-
|2010/01/16
|align="center"|2010-10
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells
|-
|2010/01/15
|align="center"|2010-09
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions
|-
|2010/01/14
|align="center"|2010-08
|chemogenomic_profiling_predicts_antifungal_synergies
|-
|2010/01/13
|align="center"|2010-07
|edgetic_perturbation_models_of_human_inherited_disorders
|-
|2010/01/12
|align="center"|2010-06
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans
|-
|2010/01/11
|align="center"|2010-05
|predicting_new_molecular_targets_for_known_drugs.pdf
Reference:SEA(Similarity Ensemble Approach)
|-
|2010/01/09
|align="center"|2010-04
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance
|-
|2010/01/08
|align="center"|2010-03
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer
|-
|2010/01/07
|align="center"|2010-02
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network
|-
|2010/01/06
|align="center"|2010-01
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs
|}

Journal Club

2018-05-07T06:10:04Z

Dreadcupper:

{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2018
|-
!scope="col" style="padding:.4em" |Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
|-
|style="padding:.4em;" rowspan=2|2018/06/14
|style="padding:.4em;"|18-12
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=A+pan-cancer+analysis+of+enhancer+expression+in+nearly+9000+patient+samples A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.]
|-
|style="padding:.4em;"|18-11
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Machine+learning+identifies+stemness+features+associated+with+oncogenic+dedifferentiation Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.]
|-
|style="padding:.4em;" rowspan=2|2018/06/07
|style="padding:.4em;"|18-10
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[hhttps://www.ncbi.nlm.nih.gov/pubmed/?term=Developmental+and+oncogenic+programs+in+H3K27M+gliomas+dissected+by+single-cell+RNA-seq Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq.]
|-
|style="padding:.4em;"|18-9
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Chemoresistance+evolution+in+triple-negative+breast+cancer+delineated+by+single-cell+sequencing Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing.]
|-
|style="padding:.4em;" rowspan=2|2018/05/31
|style="padding:.4em;"|18-8
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Mapping+human+pluripotent+stem+cell+differentiation+pathways+using+high+throughput+single-cell+RNA-sequencing Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing.]
|-
|style="padding:.4em;"|18-7
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=A+single-cell+RNA-seq+survey+of+the+developmental+landscape+of+the+human+prefrontal+cortex A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex.]
|-
|style="padding:.4em;" rowspan=2|2018/05/24
|style="padding:.4em;"|18-6
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Single-cell+RNA+sequencing+identifies+celltype-specific+cis-eQTLs+and+co-expression+QTLs Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs.]
|-
|style="padding:.4em;"|18-5
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=FOCS%3A+a+novel+method+for+analyzing+enhancer+and+gene+activity+patterns+infers+an+extensive+enhancer-promoter+map FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map.]
|-
|style="padding:.4em;" rowspan=2|2018/05/17
|style="padding:.4em;"|18-4
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/29149608 A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.]
|-
|style="padding:.4em;"|18-3
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/29610481 A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.]
|-
!scope="col" style="padding:.4em" |Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
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|style="padding:.4em;" rowspan=2|2018/05/20
|style="padding:.4em;"|18-2
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=Inferring+regulatory+element+landscapes+and+transcription+factor+networks+from+cancer+methylomes Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.]
|-
|style="padding:.4em;"|18-1
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/28129544 Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma.]
|}
{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2017
|-
!scope="col" style="padding:.4em" |Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
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|style="padding:.4em;" rowspan=2|2017/06/28
|style="padding:.4em;"|17-36
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/28104840 Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy.]
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|style="padding:.4em;"|17-35
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27240091 Landscape of tumor-infiltrating T cell repertoire of human cancers.]
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|style="padding:.4em;" rowspan=2|2017/06/14
|style="padding:.4em;"|17-34
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2015/09/01/025908 The landscape of T cell infiltration in human cancer and its association with antigen presenting gene expression.]
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|style="padding:.4em;"|17-33
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.08.052 A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.]
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|style="padding:.4em;" rowspan=2|2017/06/07
|style="padding:.4em;"|17-32
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.tandfonline.com/doi/full/10.1080/2162402X.2016.1253654 Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis.]
|-
|style="padding:.4em;"|17-31
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.celrep.2016.03.075 Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.]
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|style="padding:.4em;" rowspan=2|2017/05/31
|style="padding:.4em;"|17-30
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.02.065 Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma.]
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|style="padding:.4em;"|17-29
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.celrep.2016.12.019 Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade.]
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|style="padding:.4em;" rowspan=2|2017/05/24
|style="padding:.4em;"|17-28
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.12.022 Systemic Immunity Is Required for Effective Cencer Immunotherapy.]
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|style="padding:.4em;"|17-27
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.10.020 Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.]
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|style="padding:.4em;" rowspan=2|2017/05/17
|style="padding:.4em;"|17-26
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.10.018 Host and Environmental Factors Influencing Individual Human Cytokine Responses.]
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|style="padding:.4em;"|17-25
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.10.017 A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans.]
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|style="padding:.4em;" rowspan=2|2017/04/26
|style="padding:.4em;"|17-24
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1038%2FNMETH.4177 Pooled CRISPR screening with single-cell transcriptome readout.]
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|style="padding:.4em;"|17-23
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.11.039 Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq.]
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|style="padding:.4em;" rowspan=2|2017/04/12
|style="padding:.4em;"|17-22
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.cell.2016.11.038 Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.]
|-
|style="padding:.4em;"|17-21
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1038%2Fnbt.3569 Wishbone identifies bifurcating developmental trajectories from single-cell data.]
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|style="padding:.4em;" rowspan=2|2017/04/05
|style="padding:.4em;"|17-20
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2017/02/21/110668 Reversed graph embedding resolves complex single-cell developmental trajectories.]
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|style="padding:.4em;"|17-19
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1038%2Fnmeth.4150 Single-cell mRNA quantification and differential analysis with Census.]
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|style="padding:.4em;" rowspan=2|2017/03/29
|style="padding:.4em;"|17-18
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1016%2Fj.celrep.2016.12.060 Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage.]
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|style="padding:.4em;"|17-17
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/26051941 Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis.]
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|style="padding:.4em;" rowspan=2|2017/03/22
|style="padding:.4em;"|17-16
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27580035 Single-cell analysis of mixed-lineage states leading to a binary cell fate choice.]
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|style="padding:.4em;"|17-15
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27281220 Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq.]
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|style="padding:.4em;" rowspan=2|2017/03/15
|style="padding:.4em;"|17-14
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/?term=10.1126%2Fscience.aad0501 Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.]
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|style="padding:.4em;"|17-13
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/26084335 Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells.]
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|style="padding:.4em;" rowspan=2|2017/02/28
|style="padding:.4em;"|17-12
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[https://www.ncbi.nlm.nih.gov/pubmed/27824113 A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions.]
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|style="padding:.4em;"|17-11
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[//pubmed.gov/27851969 Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types.]
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|style="padding:.4em;" rowspan=2|2017/02/21
|style="padding:.4em;"|17-10
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2016/12/30/097451 Convergence of dispersed regulatory mutations predicts driver genes in prostate cancer.]
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|style="padding:.4em;"|17-09
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[//pubmed.gov/27723759 Chromatin structure-based prediction of recurrent noncoding mutations in cancer.]
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|style="padding:.4em;" rowspan=2|2017/02/07
|style="padding:.4em;"|17-08
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2016/11/17/088286 Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade.]
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|style="padding:.4em;"|17-07
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://biorxiv.org/content/early/2016/11/28/090134 Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer.]
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|style="padding:.4em;" rowspan=1|2017/01/31
|style="padding:.4em;"|17-06
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/27912059 Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations.]
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|style="padding:.4em;" rowspan=1|2017/01/24
|style="padding:.4em;"|17-05
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/27851914 Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells.]
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|style="padding:.4em;" rowspan=2|2017/01/17
|style="padding:.4em;"|17-04
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/25938943 Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C]
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|style="padding:.4em;"|17-03
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/27306882 CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.]
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|style="padding:.4em;" rowspan=1|2017/01/10
|style="padding:.4em;"|17-02
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/26527291 ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis]
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|style="padding:.4em;" rowspan=1|2017/01/03
|style="padding:.4em;"|17-01
|style="padding:.4em;"|SH Lee
|style="padding:.4em;text-align:left"|
[//www.ncbi.nlm.nih.gov/pubmed/26287467 Single-cell messenger RNA sequencing reveals rare intestinal cell types]
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{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2016
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!scope="col" style="padding:.4em" |Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
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|style="padding:.4em;" rowspan=1|2016/12/27
|style="padding:.4em;"|2016-31
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/25664528 Decoding the regulatory network of early blood development from single-cell gene expression measurements.]
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|style="padding:.4em;" rowspan=1|2016/12/6
|style="padding:.4em;"|2016-30
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26299571 Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.]
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|style="padding:.4em;" rowspan=1|2016/11/29
|style="padding:.4em;"|2016-29
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/24658644 The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.]
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|style="padding:.4em;" rowspan=1|2016/11/22
|style="padding:.4em;"|2016-28
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26887813 Classification of low quality cells from single-cell RNA-seq data.]
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|style="padding:.4em;" rowspan=1|2016/11/15
|style="padding:.4em;"|2016-27
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26000487 Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.]
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|style="padding:.4em;" rowspan=1|2016/11/8
|style="padding:.4em;"|2016-26
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26000488 Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.]
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|style="padding:.4em;" rowspan=1|2016/11/1
|style="padding:.4em;"|2016-25
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27426982 Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.]
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|style="padding:.4em;" rowspan=1|2016/10/25
|style="padding:.4em;"|2016-24
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27549193 Comprehensive analyses of tumor immunity: implications for cancer immunotherapy.]
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|style="padding:.4em;" rowspan=1|2016/10/11
|style="padding:.4em;"|2016-23
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=sidespread+parainflammation Widespread parainflammation in human cancer]
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|style="padding:.4em;" rowspan=1|2016/9/27
|style="padding:.4em;"|2016-22
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27535533 Analysis of protein-coding genetic variation in 60,706 humans]
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|style="padding:.4em;" rowspan=1|2016/9/20
|style="padding:.4em;"|2016-21
|style="padding:.4em;"|SM Yang
|style="padding:.4em;text-align:left"|
Functional characterization of somatic mutations in cancer using network-based inference of protein activity
[http://www.ncbi.nlm.nih.gov/pubmed/27322546 pubmed]
[http://www.nature.com/ng/journal/v48/n8/full/ng.3593.html fulltext]
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|style="padding:.4em;" rowspan=1|2016/9/13
|style="padding:.4em;"|2016-20
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=exploiting+single-cell+expression+to+characterize Exploiting single-cell expression to characterize co-expression replicability.]
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|style="padding:.4em;" rowspan=1|2016/9/6
|style="padding:.4em;"|2016-19
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26940869 Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade]
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|style="padding:.4em;" rowspan=1|2016/8/31
|style="padding:.4em;"|2016-18
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27264179 A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors]
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|style="padding:.4em;" rowspan=1|2016/8/16
|style="padding:.4em;"|2016-17
|style="padding:.4em;"|JW Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27309802 The landscape of accessible chromatin in mammalian preimplantation embryos]
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|style="padding:.4em;" rowspan=1|2016/8/8
|style="padding:.4em;"|2016-16
|style="padding:.4em;"|EB Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27064255 Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin]
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|style="padding:.4em;" rowspan=1|2016/8/1
|style="padding:.4em;"|2016-15
|style="padding:.4em;"|MY Lee
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27040498 Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients]
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|style="padding:.4em;" rowspan=1|2016/7/25
|style="padding:.4em;"|2016-14
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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]
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|style="padding:.4em;" rowspan=1|2016/7/18
|style="padding:.4em;"|2016-13
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]
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|style="padding:.4em;" rowspan=2|2016/6/8
|style="padding:.4em;"|2016-12
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]
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|style="padding:.4em;"| 2016-11
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]
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|style="padding:.4em;" rowspan=2|2016/6/1
|style="padding:.4em;"|2016-10
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]
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|style="padding:.4em;"| 2016-9
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]
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|style="padding:.4em;" rowspan=2|2016/5/18
|style="padding:.4em;"|2016-8
|style="padding:.4em;"|CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]
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|style="padding:.4em;"| 2016-7
|style="padding:.4em;"| CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]
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|style="padding:.4em;" rowspan=2|2016/5/11
|style="padding:.4em;"|2016-6
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]
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|style="padding:.4em;"| 2016-5
|style="padding:.4em;"|DS Bae, CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]
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|style="padding:.4em;" rowspan=2|2016/5/4
|style="padding:.4em;"|2016-4
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[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]
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|style="padding:.4em;"| 2016-3
|style="padding:.4em;"|MY Lee,SM Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]
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|style="padding:.4em;" rowspan=2|2016/4/27
|style="padding:.4em;"|2016-2
|style="padding:.4em;"|CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]
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|style="padding:.4em;"| 2016-1
|style="padding:.4em;"| CY Kim,SJ Kwon
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]
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{|class=wikitable style="text-align:center;"
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|style="padding:.4em;" rowspan=2|2015/06/11
|style="padding:.4em;"|2015-55
|style="padding:.4em;"|
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[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]
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|style="padding:.4em;"|2015-54
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;" rowspan=2|2015/06/04
|style="padding:.4em;"|2015-53
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[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]
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|style="padding:.4em;"|2015-52
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[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]
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|style="padding:.4em;" rowspan=2|2015/05/28
|style="padding:.4em;"|2015-51
|style="padding:.4em;"|
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[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.]
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|style="padding:.4em;"|2015-50
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]
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|style="padding:.4em;" rowspan=2|2015/05/21
|style="padding:.4em;"|2015-49
|style="padding:.4em;"|
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[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]
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|style="padding:.4em;"|2015-48
|style="padding:.4em;"|
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[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]
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|style="padding:.4em;" rowspan=2|2015/05/14
|style="padding:.4em;"|2015-47
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[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]
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|style="padding:.4em;"|2015-46
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|style="padding:.4em;text-align:left"|
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]
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|style="padding:.4em;" rowspan=3|2015/05/07
|style="padding:.4em;"|2015-45
|style="padding:.4em;"|
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[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]
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|style="padding:.4em;"|2015-44
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]
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|style="padding:.4em;"|2015-43
|style="padding:.4em;"|
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[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]

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|style="padding:.4em;" rowspan=2|2015/04/30
|style="padding:.4em;"|2015-42
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]
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|style="padding:.4em;"|2015-41
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]
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|style="padding:.4em;" rowspan=3|2015/04/23
|style="padding:.4em;"|2015-40
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]
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|style="padding:.4em;"|2015-39
|style="padding:.4em;"|
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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.]
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|style="padding:.4em;"|2015-38
|style="padding:.4em;"|
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[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]
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|style="padding:.4em;" rowspan=2|2015/04/09
|style="padding:.4em;"|2015-37
|style="padding:.4em;"|
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[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]
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|style="padding:.4em;"|2015-36
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]
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|style="padding:.4em;" rowspan=2|2015/04/02
|style="padding:.4em;"|2015-35
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]
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|style="padding:.4em;"|2015-34
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]
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|style="padding:.4em;" rowspan=2|2015/03/26
|style="padding:.4em;"|2015-33
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]
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|style="padding:.4em;"|2015-32
|style="padding:.4em;"|
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[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.]
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|style="padding:.4em;" rowspan=2|2015/03/19
|style="padding:.4em;"|2015-31
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2015-30
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]
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|style="padding:.4em;" rowspan=3|2015/03/12
|style="padding:.4em;"|2015-29
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|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]
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|style="padding:.4em;"|2015-28
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|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]
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|style="padding:.4em;"|2015-27
|style="padding:.4em;"|
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]
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|style="padding:.4em;" rowspan=3|2015/03/09
|style="padding:.4em;"|2015-26
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]
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|style="padding:.4em;"|2015-25
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2015-24
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]
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|style="padding:.4em;" rowspan=3|2015/03/02
|style="padding:.4em;"|2015-23
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]
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|style="padding:.4em;"|2015-22
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2015-21
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]
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|style="padding:.4em;" rowspan=3|2015/02/24
|style="padding:.4em;"|2015-20
|style="padding:.4em;"|ER Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]
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|style="padding:.4em;"|2015-19
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]
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|style="padding:.4em;"|2015-18
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]
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|style="padding:.4em;" rowspan=3|2015/02/16
|style="padding:.4em;"|2015-17
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]
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|style="padding:.4em;"|2015-16
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]
|-
|style="padding:.4em;"|2015-15
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]
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|style="padding:.4em;" rowspan=4|2015/02/02
|style="padding:.4em;"|2015-14
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]
|-
|style="padding:.4em;"|2015-13
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]
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|style="padding:.4em;"|2015-12
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]
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|style="padding:.4em;"|2015-11
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;" rowspan=5|2015/01/26
|style="padding:.4em;"|2015-10
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]
|-
|style="padding:.4em;"|2015-09
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]
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|style="padding:.4em;"|2015-08
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]
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|style="padding:.4em;"|2015-07
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]
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|style="padding:.4em;"|2015-06
|style="padding:.4em;"|BH Kang
|style="padding:.4em;text-align:left"|
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]
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|style="padding:.4em;" rowspan=3|2015/01/12
|style="padding:.4em;"|2015-05
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]
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|style="padding:.4em;"|2015-04
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]
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|style="padding:.4em;"|2015-03
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]
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|style="padding:.4em;" rowspan=2|2015/01/05
|style="padding:.4em;"|2015-02
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]
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|style="padding:.4em;"|2015-01
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[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.]
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{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2014
|-
!scope="col" style="padding:.4em" | Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
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|style="padding:.4em;" rowspan=2|2014/12/23
|style="padding:.4em;"|2014-41
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]
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|style="padding:.4em;"|2014-40
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]
|-
|style="padding:.4em;" rowspan=4|2014/12/09
|style="padding:.4em;"|2014-39
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]
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|style="padding:.4em;"|2014-38
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]
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|style="padding:.4em;"|2014-37
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]
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|style="padding:.4em;"|2014-36
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]
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|style="padding:.4em;" rowspan=2|2014/12/02
|style="padding:.4em;"|2014-35
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]
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|style="padding:.4em;"|2014-34
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]
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|style="padding:.4em;" rowspan=2|2014/11/25
|style="padding:.4em;"|2014-33
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2014-32
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]
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|style="padding:.4em;" rowspan=2|2014/11/18
|style="padding:.4em;"|2014-31
|style="padding:.4em;"|SM Yang
|style="padding:.4em;text-align:left"|
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]
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|style="padding:.4em;"|2014-30
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]
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|style="padding:.4em;" rowspan=3|2014/11/11
|style="padding:.4em;"|2014-29
|style="padding:.4em;"|DS Bae
|style="padding:.4em;text-align:left"|
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]
|-
|style="padding:.4em;"|2014-28
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]
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|style="padding:.4em;"|2014-27
|style="padding:.4em;"|HH Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]
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|style="padding:.4em;" rowspan=2|2014/11/04
|style="padding:.4em;"|2014-26
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]
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|style="padding:.4em;"|2014-25
|style="padding:.4em;"|JH Shin
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]
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|style="padding:.4em;" rowspan=2|2014/10/28
|style="padding:.4em;"|2014-24
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]
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|style="padding:.4em;"|2014-23
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;" rowspan=2|2014/09/30
|style="padding:.4em;"|2014-22
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]
|-
|style="padding:.4em;"|2014-21
|style="padding:.4em;"|KS Kim
|style="padding:.4em;text-align:left"|
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]
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|style="padding:.4em;" rowspan=2|2014/09/23
|style="padding:.4em;"|2014-20
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[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.]
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|style="padding:.4em;"|2014-19
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]
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|style="padding:.4em;" rowspan=2|2014/09/16
|style="padding:.4em;"|2014-18
|style="padding:.4em;"|JH Shin
|style="padding:.4em;text-align:left"|
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]
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|style="padding:.4em;"|2014-17
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]
|-
|style="padding:.4em;" rowspan=2|2014/09/02
|style="padding:.4em;"|2014-16
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]
|-
|style="padding:.4em;"|2014-15
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]
|-
|style="padding:.4em;" rowspan=2|2014/08/19
|style="padding:.4em;"|2014-14
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]
|-
|style="padding:.4em;"|2014-13
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]
|-
|style="padding:.4em;" rowspan=2|2014/08/12
|style="padding:.4em;"|2014-12
|style="padding:.4em;"|HS Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]
|-
|style="padding:.4em;"|2014-11
|style="padding:.4em;"|HJ Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]
|-
|style="padding:.4em;" rowspan=2|2014/08/05
|style="padding:.4em;"|2014-10
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]
|-
|style="padding:.4em;"|2014-9
|style="padding:.4em;"|JE Shim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]
|-
|style="padding:.4em;" rowspan=3|2014/07/29
|style="padding:.4em;"|2014-8
|style="padding:.4em;"|CY Kim
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]
|-
|style="padding:.4em;"|2014-7
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]
|-
|style="padding:.4em;"|2014-6
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]
|-
|style="padding:.4em;" rowspan=3|2014/07/22
|style="padding:.4em;"|2014-5
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]
|-
|style="padding:.4em;"|2014-4
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]
|-
|style="padding:.4em;"|2014-3
|style="padding:.4em;"|AR Cho
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]
|-
|style="padding:.4em;" rowspan=2|2014/07/15
|style="padding:.4em;"|2014-2
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]
|-
|style="padding:.4em;"|2014-1
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]
|}
{|class=wikitable style="text-align:center;"
|+style="text-align:left;font-size:12pt" | 2013
|-
!scope="col" style="padding:.4em" | Date
!scope="col" style="padding:.4em" | Paper<br/>index
!scope="col" style="padding:.4em" | Presenter
!scope="col" style="padding:.4em" | Paper title
|-
|style="padding:.4em;" rowspan=2|2013/06/26
|style="padding:.4em;"|2013-31
|style="padding:.4em;"|HJ Han
|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]
|-
|style="padding:.4em;"|2013-30
|style="padding:.4em;"|YH Ko
|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]
|-
|style="padding:.4em;" rowspan=2|2013/06/04
|style="padding:.4em;"|2013-29
|style="padding:.4em;"|KS Kim
|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]
|-
|style="padding:.4em;"|2013-28
|style="padding:.4em;"|ER Kim
|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]
|-
|style="padding:.4em;" rowspan=2|2013/05/28
|style="padding:.4em;"|2013-27
|style="padding:.4em;"|YH Ko
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]
|-
|style="padding:.4em;"|2013-26
|style="padding:.4em;"|JE Shim
|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]
|-
|style="padding:.4em;" rowspan=2|2013/05/21
|style="padding:.4em;"|2013-25
|style="padding:.4em;"|HJ Han
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]
|-
|style="padding:.4em;"|2013-24
|style="padding:.4em;"|T Lee
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]

|-
|style="padding:.4em;" rowspan=2|2013/05/14
|style="padding:.4em;"|2013-23
|style="padding:.4em;"|JE Shim
|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]

|-
|style="padding:.4em;"|2013-22
|style="padding:.4em;"|HJ Kim
|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]
|-
|style="padding:.4em;" rowspan=2|'''2013/05/07'''
|style="padding:.4em;"|2013-21
|style="padding:.4em;"|ER Kim
|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]
|-
|style="padding:.4em;"|2013-20
|style="padding:.4em;"|HS Shim
|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]
|-
|style="padding:.4em;"|2013/04/09
|style="padding:.4em;"|2013-19
|style="padding:.4em;"|HJ Kim
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]
|-
|style="padding:.4em;"|2013/04/02
|style="padding:.4em;"|2013-18
|style="padding:.4em;"|HJ Kim
|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]
|-
|style="padding:.4em;" |2013/03/12
|style="padding:.4em;"|2013-17
|style="padding:.4em;"| ER Kim
|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]
|-
|style="padding:.4em;" rowspan=1|2013/03/05
|style="padding:.4em;"|2013-16
|style="padding:.4em;"| ER Kim
|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]
|-
|style="padding:.4em;" rowspan=3|2013/02/21
|style="padding:.4em;"|2013-15
|style="padding:.4em;"| KS Kim
|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]
|-
|style="padding:.4em;"|2013-14
|style="padding:.4em;"| KS Kim
|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]
|-
|style="padding:.4em;"|2013-13
|style="padding:.4em;"| HJ Han
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]
|-
|style="padding:.4em;" rowspan=3|2013/02/15
|style="padding:.4em;"|2013-12
|style="padding:.4em;"| HJ Han
|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]
|-
|style="padding:.4em;"|2013-11
|style="padding:.4em;"| JE Shim, CY Kim
|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]
|-
|style="padding:.4em;"|2013-10
|style="padding:.4em;"|HJ Han, JH Kim
|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]
|-
|style="padding:.4em;" rowspan=3|2013/02/08
|style="padding:.4em;"|2013-09
|style="padding:.4em;"|HJ Kim
|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]
|-
|style="padding:.4em;"|2013-08
|style="padding:.4em;"|JE Shim, CY Kim
|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]
|-
|style="padding:.4em;"|2013-07
|style="padding:.4em;"|HJ Han, JH Kim
|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]
|-
|style="padding:.4em;" rowspan=3|2013/01/25
|style="padding:.4em;"|2013-06
|style="padding:.4em;"|HJ Han, '''JH Kim'''
|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]
|-
|style="padding:.4em;"|2013-05
|style="padding:.4em;"|'''ER Kim''', HS Shim
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]
|-
|style="padding:.4em;"|2013-04
|style="padding:.4em;"|'''HJ Han''', JH Kim
|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]

|-
|style="padding:.4em;" rowspan=2|2013/01/18
|style="padding:.4em;"|2013-03
|style="padding:.4em;"|KS Kim, '''TH Kim'''
|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]
|-
|style="padding:.4em;"|2013-02
|style="padding:.4em;"|'''HJ Han''', JH Kim
|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]
|-
|style="padding:.4em;" rowspan=1|2013/01/11
|style="padding:.4em;"|2013-01
|style="padding:.4em;"| '''JE Shim''', CY Kim
|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]
|}

2012
{|border ="1"
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title
|-
|rowspan = "1"|2013/01/11
|align ="center"|2012-81
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]
|-
|rowspan = "1"|2012/12/04
|align ="center"|2012-80
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]
|-
|rowspan = "2"|2012/11/20
| align="center"|2012-79
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]
|-
| align="center"|2012-78
|[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]
|-
|rowspan = "2"|2012/11/06
| align="center"|2012-77
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]
|-
| align="center"|2012-76
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes]
|-
|rowspan = "6" |2012/07/19
| align="center"|2012-75
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]
|-
| align="center"|2012-74
|[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]
|-
| align="center"|2012-73
|[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]
|-
| align="center"|2012-72
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]
|-
| align="center"|2012-71
|[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]
|-
| align="center"|2012-70
|[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]
|-
|rowspan = "8" |2012/07/16
| align="center"|2012-69
|[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]
|-
| align="center"|2012-66
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]
|-
| align="center"|2012-65
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]
|-
| align="center"|2012-64
|[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]
|-
|align="center"|2012-63
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]
|-
|align="center"|2012-62
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]
|-
|align="center"|2012-61
|[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]
|-
|align="center"|2012-60
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]
|-
|rowspan = "3" |2012/07/13
|align="center"|2012-59
|[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]
|-
| align="center"|2012-58
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]
|-
|align="center"|2012-57
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]
|-
|rowspan = "4" |2012/07/12
|align="center"|2012-56
|[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]
|-
|align="center"|2012-55
|[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]
|-
| align="center"|2012-54
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]
|-
|align="center"|2012-53
|[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]
|-
|rowspan = "6" |2012/07/09
|align="center"|2012-52
|[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]
|-
|align="center"|2012-51
|[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]
|-
| align="center"|2012-50
|[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]
|-
|align="center"|2012-49
|[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]
|-
|align="center"|2012-48
|[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]
|-
|align="center"|2012-47
|[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]
|-
|rowspan = "6" |2012/07/06
| align="center"|2012-46
|[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)]
|-
|align="center"|2012-45
|[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]
|-
|align="center"|2012-44
|[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]
|-
|align="center"|2012-43
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]
|-
| align="center"|2012-42
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]
|-
|align="center"|2012-41
|[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]
|-
|rowspan = "6" |2012/07/02
|align="center"|2012-40
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]
|-
|align="center"|2012-39
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]
|-
| align="center"|2012-38
|[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]
|-
|align="center"|2012-37
|[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]
|-
|align="center"|2012-36
|[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]
|-
|align="center"|2012-35
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]
|-
|rowspan = "3" |2012/03/05
| align="center"|2012-34
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]
|-
|align="center"|2012-33
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]
|-
|align="center"|2012-32
|[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 ]
|-
|rowspan = "7" |2012/02/27<br />2012/02/28
| align="center"|2012-31
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]
|-
|align="center"|2012-30
|[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]
|-
|align="center"|2012-29
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]
|-
|align="center"|2012-28
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]
|-
|align="center"|2012-27
|[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]
|-
|align="center"|2012-26
|[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]
|-
|align="center"|2012-25
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]
|-
|rowspan = "5" |2012/02/06
| align="center"|2012-24
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]
|-
|align="center"|2012-23
|[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]
|-
|align="center"|2012-22
|[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]
|-
|align="center"|2012-21
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]
|-
|align="center"|2012-20
|[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]
|-
|rowspan = "5" |2012/01/30
|align="center"|2012-19
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]
|-
|align="center"|2012-18
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]
|-
|align="center"|2012-17
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]
|-
|align="center"|2012-16
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]
|-
|align="center"|2012-15
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]
|-
|rowspan = "3" |2012/01/09
|align="center"|2012-14
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]
|-
|align="center"|2012-13
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]
|-
|align="center"|2012-12
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]
|-
|rowspan = "6" |2012/01/09<br />2012/01/16
| align="center"|2012-11
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]
|-
|align="center"|2012-10
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]
|-
|align="center"|2012-09
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]
|-
|align="center"|2012-08
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]
|-
|align="center"|2012-07
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]
|-
|align="center"|2012-06
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]
|-
|rowspan = "3" |2012/01/09<br />2012/01/16
|align="center"|2012-05
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]
|-
|align="center"|2012-04
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]
|-
|align="center"|2012-03
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]
|-
|rowspan = "2" |2012/01/09<br />2012/01/16
|align="center"|2012-02
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]
|-
|align="center"|2012-01
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]
|}
2011
{|border ="1"
|style="color:black; background-color:#dcdcdc;" align="center" |Date
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title
|-
|rowspan = "6" |2011/11/28
|align="center"|2011-49
|[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]
|-
|align="center"|2011-48
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]
|-
|align="center"|2011-47
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]
|-
|align="center"|2011-46
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]
|-
|align="center"|2011-45
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]
|-
|align="center"|2011-44
|[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]
|-
|rowspan = "3" |2011/11/14
|align="center"|2011-43
|[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]
|-
|align="center"|2011-42
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]
|-
|align="center"|2011-41
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]
|-
|rowspan = "4" |2011/11/07
|align="center"|2011-40
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]
|-
|align="center"|2011-39
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]
|-
|align="center"|2011-38
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]
|-
|align="center"|2011-37
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]
|-
|rowspan = "3" |2011/11/07
|align="center"|2011-36
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]
|-
|align="center"|2011-35
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]
|-
|align="center"|2011-34
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]
|-
|rowspan = "3" |2011/10/05
|align="center"|2011-33
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]
|-
|align="center"|2011-32
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]
|-
|align="center"|2011-31
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]
|-
|rowspan = "4" |2011/10/04
|align="center"|2011-30
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]
|-
|align="center"|2011-29
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]
|-
|align="center"|2011-28
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]
|-
|align="center"|2011-27
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]
|-
|rowspan = "2" |2011/09/19
|align="center"|2011-26
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]
|-
|align="center"|2011-25
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]
|-
|rowspan = "2" |2011/09/05
|align="center"|2011-24
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]
|-
|align="center"|2011-23
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]
|-
|rowspan = "2" |2011/09/22
|align="center"|2011-22
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]
|-
|align="center"|2011-21
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]
|-
|2011/06/20
|align="center"|2011-20
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]
|-
|rowspan = "2" |2011/03/30
|align="center"|2011-19
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]
|-
|align="center"|2011-18
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]
|-
|rowspan = "2" |2011/03/16
|align="center"|2011-17
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']
|-
|align="center"|2011-16
|[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]
|-
|rowspan = "3" |2011/04/25
|align="center"|2011-15
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]
|-
|align="center"|2011-14
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]
|-
|align="center"|2011-13
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]
|-
|rowspan = "2" |2011/04/11
|align="center"|2011-12
|[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]
|-
|align="center"|2011-11
|***Changed!***
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]
|-
|rowspan = "2"|2011/03/28
|align="center"|2011-10
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]
|-
|align="center"|2011-09
|[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"|2011/03/14
|align="center"|2011-08
|[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]
|-
|align="center"|2011-07
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]
|-
|rowspan = "2"|2011/02/28
|align="center"|2011-06
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]
|-
|align="center"|2011-05
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]
|-
|2011/02/21
|align="center"|2011-04
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]
|-
|2011/02/14
|align="center"|2011-03
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]
|-
|rowspan = "2"|2011/01/31
|align="center"|2011-02
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]
|-
|align="center"|2011-01
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]
|}
2010
{|border ="1"
|style="color:black; background-color:#dcdcdc;" align="center" |Date
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title
|-
|rowspan = "2"|2010/12/27
|align="center"|2010-29
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]
|-
|align="center"|2010-28
|[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"|2010/11/15
|align="center"|2010-27
|[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]
|-
|align="center"|2010-26
|[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"|2010/11/01
|align="center"|2010-25
|[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]
|-
|align="center"|2010-24
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]
|-
|2010/10/11
|align="center"|2010-23
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]
|-
|rowspan = "2"|2010/09/13
|align="center"|2010-22
|[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]
|-
|align="center"|2010-21
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]
|-
|2010/05/26
|align="center"|2010-20
|[[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]]
|-
|2010/05/19
|align="center"|2010-19
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]
|-
|2010/04/21
|align="center"|2010-18
|[[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]]
|-
|2010/04/14
|align="center"|2010-17
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]
|-
|rowspan = "2" |2010/04/07
|align="center"|2010-16
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]
|-
|align="center"|2010-15
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]
|-
|rowspan="2"|2010/03/31
|align="center"|2010-14
|[[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]]
|-
|align="center"|2010-13
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]
|-
|2010/03/24
|align="center"|2010-12
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]
|-
|2010/01/18
|align="center"|2010-11
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies
|-
|2010/01/16
|align="center"|2010-10
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells
|-
|2010/01/15
|align="center"|2010-09
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions
|-
|2010/01/14
|align="center"|2010-08
|chemogenomic_profiling_predicts_antifungal_synergies
|-
|2010/01/13
|align="center"|2010-07
|edgetic_perturbation_models_of_human_inherited_disorders
|-
|2010/01/12
|align="center"|2010-06
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans
|-
|2010/01/11
|align="center"|2010-05
|predicting_new_molecular_targets_for_known_drugs.pdf
Reference:SEA(Similarity Ensemble Approach)
|-
|2010/01/09
|align="center"|2010-04
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance
|-
|2010/01/08
|align="center"|2010-03
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer
|-
|2010/01/07
|align="center"|2010-02
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network
|-
|2010/01/06
|align="center"|2010-01
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs
|}

File:2018 NBLexperiment teaching material.pdf

2018-04-03T06:54:23Z

Dreadcupper: Dreadcupper uploaded a new version of "File:2018 NBLexperiment teaching material.pdf"

Teaching

2018-04-03T04:41:05Z

Dreadcupper:

== Data for 2018 netbiolab experiment==
[//netbiolab.org/wiki/images/1/12/2018_NBLexperiment_teaching_material.pdf 2018 netbiolab experiment teaching material]

[//netbiolab.org/wiki/images/1/18/2018_NBLexperiment_training_material.zip 2018 netbiolab experiment training material]

== Data for other teaching materials ==
[[Teaching Materials for Students]]

[https://www.netbiolab.org/wiki/images/7/7b/2017_BIML_0216_2.zip BIML2017 practice 2 PPT file & python scripts]

[http://www.netbiolab.org/wiki/images/4/4b/Practice1.pdf BIML2016 practice 1 PPT file]

[http://www.netbiolab.org/wiki/images/c/c0/Biml_python_scripts.zip BIML2016 practice 2 python scripts]

<div>{{#widget:AddHtml|content=<img src="../wiki/wordcloud_2013_2017.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div>

Teaching Materials for Students

2018-04-03T04:40:22Z

Dreadcupper:

== 2018 Bioinformatics class data ==
[//netbiolab.org/wiki/Kallisto_materials.zip data for Kallisto]

[//netbiolab.org/wiki/WebMev_materials.zip data for WebMev]

== Data for previous classes ==
[//netbiolab.org/wiki/images/d/d0/2017nblexperiment.zip 2017 netbiolab experiment sample]

[//netbiolab.org/wiki/images/f/f9/2016nblexperiment.zip 2016 netbiolab experiment sample]

[//netbiolab.org/wiki/images/2/2c/2015nblexperiment.zip 2015 netbiolab experiment sample]

[//netbiolab.org/wiki/images/9/91/2014NetbioSampleNetwork.zip 2014 netbiolab experiment sample]

[//netbiolab.org/wiki/images/4/4c/LAB6_instructions.pdf experiment demonstration file]

Teaching Materials for Students

2018-04-03T04:24:37Z