https://netbiolab.org/wiki/api.php?action=feedcontributions&feedformat=atom&user=Hhj6212
Network Biology Lab - User contributions [en]
2026-04-29T07:35:51Z
User contributions
MediaWiki 1.31.16
https://netbiolab.org/wiki/index.php?title=Software&diff=4984
Software
2019-06-07T09:57:44Z
<p>Hhj6212: /* Network Medicine Tools */</p>
<hr />
<div>__NOTOC__<br />
=='''Network Medicine Tools '''==<br />
[[File:HumanNet_logo_with_title.png|150px|link=http://www.inetbio.org/humannet]]'''HumanNet''': Human gene networks for disease research<br />
<br />
<br />
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST''': Curated TF-target interaction networks in human and mouse<br />
<br />
<br />
[[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation data<br />
<br />
<br />
[[File:GWAB_logo.png |150px|link=http://www.inetbio.org/gwab]] '''GWAB''': A web server for network-based boosting of human genome-wide association data<br />
<br />
<br />
[[File:Coexpedia.png |150px|link=http://www.coexpedia.org]] '''COEXPEDIA''': Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)<br />
<br />
<br />
[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN''': Network-assisted prediction of disease pathways in model organisms<br />
<br />
<br />
[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only)<br />
<br />
[[File:Ngsea logo1.png |150px|link=https://www.inetbio.org/ngsea/]] '''NGSEA''': Network-augmented gene set enrichment analysis tool<br />
<br />
=='''Co-functional Gene Networks'''==<br />
<br />
==''Laboratory Animals''==<br />
{|border="0" width="400"<br />
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]<br />
|align="center"|[[file:danionet_logo.png|150px|link=http://www.inetbio.org/danionet]]<br />
|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]<br />
|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]<br />
|-<br />
|align="center"|''Mus musculus''<br />
|align="center"|''Danio rerio''<br />
|align="center"|''Drosophila melanogaster''<br />
|align="center"|''Caenorhabditis elegans''<br />
|}<br />
<br />
==''Plants''==<br />
{|border="0" width="400"<br />
|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]]<br />
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=http://www.inetbio.org/maizenet]]<br />
|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]<br />
|align="center"|[[File:WheatNet_logo.png|150px|link=http://www.inetbio.org/wheatnet]]<br />
|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]<br />
|align="center"|[[File:Tomatonet_logo.png|150px|link=http://www.inetbio.org/tomatonet]]<br />
|-<br />
|align="center"|''Arabidopsis thaliana''<br />
|align="center"|''Zea mays''<br />
|align="center"|''Oryza sativa''<br />
|align="center"|''Triticum aestivum''<br />
|align="center"|''Glycine max''<br />
|align="center"|''Solanum lycopersicum''<br />
|}<br />
<br />
==''Fungi''==<br />
{|border="0" width="200"<br />
|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]]<br />
|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]]<br />
|-<br />
|align="center"|''Saccharomyces cerevisiae''<br />
|align="center"|''Cryptococcus neoformans''<br />
|}<br />
<br />
==''Bacteria''==<br />
{|border="0" width="200"<br />
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]]<br />
|align="center"|[[File:Staphnet_logo.JPG|150px|link=http://www.inetbio.org/staphnet]]<br />
|align="center"|[[File:KlebNet_logo.png|150px|link=http://www.inetbio.org/klebnet]]<br />
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]<br />
|align="center"|[[File:XooNet_logo.png|150px|link=http://www.inetbio.org/xoonet]]<br />
|-<br />
|align="center"|''Pseudomonas aeruginosa (human pathogen)''<br />
|align="center"|Methicillin-resistant ''Staphylococcus aureus (human pathogen)''<br />
|align="center"|''Klebsiella pneumoniae (human pathogen)''<br />
|align="center"|''Escherichia coli (popular lab/factory bacterial species)''<br />
|align="center"|''Xanthomonas oryzae pv. oryzae (rice pathogen)''<br />
|}<br />
<br />
==''Build your own co-functional networks''==<br />
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]]<br />
'''JiffyNet''': Instant gene network building server for newly sequenced species<br />
<br />
<br />
<br />
<br />
=='''Network-augmented GWAS Analysis for Arabidopsis'''==<br />
[[File:araGWAB_logo.png|150px|link=http://www.inetbio.org/aragwab]]<br />
'''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana''<br />
<br />
<br />
<br />
<br />
=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==<br />
[[WMI|<big>'''Project Page'''</big>]]<br />
<br />
<br />
=='''Domain2Pathway by Pathway Specificity (PS) '''==<br />
[[PS|<big>'''Project Page'''</big>]]</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=File:Ngsea_logo1.png&diff=4983
File:Ngsea logo1.png
2019-06-07T09:56:25Z
<p>Hhj6212: Ngsea_logo1.png</p>
<hr />
<div>Ngsea_logo1.png</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=People&diff=4433
People
2017-05-28T14:43:10Z
<p>Hhj6212: </p>
<hr />
<div>__NOTOC__<br />
=='''Principal Investigator'''==<br />
{|border="0" width="150"<br />
|align="center"|[[File:이인석-2011사진.jpg|77px|link=people:IS_Lee]]<br />
|-<br />
|align="center"|[[people:IS_Lee|Insuk Lee]]<br />
|-<br />
|}<br />
<br />
=='''Research Professor/Postdoc Fellow/Research Staff'''==<br />
{|border="0" width="500"<br />
|align="center"|[[File:People_JE_Shim_EDIT.JPG|70px|link=people:JE_Shim]]<br />
|align="center" |[[File:Tak_sajin3.jpg|70px|link=people:T_Lee]]<br />
|align="center"|[[File:Smyang.jpg|70px|link=people:SM_Yang]]<br />
|align="center"|[[File:SYLee.jpg|70px|link=people:SY_Lee]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Jung Eun Shim]]<br />
|align="center"|[[people:T_Lee|Tak Lee]]<br />
|align="center"|[[people:SM_Yang|Sunmo Yang]]<br />
|align="center"|[[people:SY_Lee|Sangyoung Lee]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Research Professor]]<br />
|align="center"|[[people:T_Lee|Postdoc Fellow]]<br />
|align="center"|[[people:SM_Yang|Bioinformatics Programmer<br/>System Administrator]]<br />
|align="center"|[[people:SY_Lee|Senior Research Assistant]]<br />
|}<br />
<br />
=='''Graduate Students'''==<br />
{|border="0" width="900"<br />
<br />
|align="center" |[[File:heonjong.jpg|70px|link=people:HJ_Han]]<br />
|align="center" |[[File:People_KSKim.jpg|70px|link=people:KS_Kim]]<br />
|align="center"|[[File:배다솜.jpg|70px|link=People:DS Bae]]<br />
|align="center"|[[File:CY KIM.jpg|70px|link=People:CY_Kim]]<br />
|align="center"|[[File:Muyoung_Lee_2.jpg|70px|link=People:M_Lee]]<br />
|align="center"|[[File:Cho_JW.png|70px|link=People:J_Cho]]<br />
|align="center"|[[File:kim_EB.jpg|70px|link=People:E_Kim]]<br />
|align="center"|[[File:SHLee_outside.jpg|70px|link=People:S_Lee]]<br />
|-<br />
<br />
|align="center"|[[people:HJ_Han|Heonjong Han]]<br />
|align="center"|[[people:KS_Kim|Kyungsoo Kim]]<br />
|align="center"|[[People:DS Bae|Dasom Bae]]<br />
|align="center"|[[People:CY Kim|Chan Yeong Kim]]<br />
|align="center"|[[People:M_Lee|Muyoung Lee]]<br />
|align="center"|[[People:J_Cho|Jae Won Cho]]<br />
|align="center"|[[People:E_Kim|Eunbeen Kim]]<br />
|align="center"|[[People:S_Lee|Sungho Lee]]<br />
|-<br />
<br />
|align="center"|[[People:HJ_Han|PhD candidate<br/>(2013.3 - )]]<br />
|align="center"|[[people:KS_Kim|PhD candidate<br/>(2013.3 - )]]<br />
|align="center"|[[people:DS Bae|PhD course<br/>(2014.9 - )]]<br />
|align="center"|[[people:CY Kim|PhD course<br/>(2015.3 - )]]<br />
|align="center"|[[people:M_Lee|PhD course<br/>(2016.3 - )]]<br />
|align="center"|[[people:J_Cho|PhD course<br/>(2016.9 - )]]<br />
|align="center"|[[people:E_Kim|PhD course<br/>(2016.9 - )]]<br />
|align="center"|[[People:S_Lee|PhD course<br/>(2017.3 - )]]<br />
|}<br />
<br />
=='''Undergraduate Students'''==<br />
*Yaeji Kim<br />
<br />
=='''Visiting scientists/students'''==<br />
<br />
=='''Alumni'''==<br />
*Former Post-docs and Staff Scientists<br />
**Taeyun Oh (2009.5-2011.12), currently Deputy Principal Consultant, [http://www.insilicogen.com INSILICOGEN], Korea <br />
**Sohyun Hwang (2010.3-2015.8), currently Assistant Professor, [http://bt.cha.ac.kr/ Department of Biomedical Science, CHA University], Korea <br />
**Samuel Beck (2011.2-2011.12), currently Assistant Professor of Computational Biology, [https://mdibl.org/ The Mount Desert Island Biological Laboratory], Maine, USA <br />
**Jawon Song (2011.1-2012.5), currently Research Associate, [https://www.tacc.utexas.edu/about/directory/jawon-song Texas Advanced Computing Center], Austin, TX, USA<br />
**Yoonhee Ko (2012.8-2014.2), currently Assistant Professor, [http://bme.hufs.ac.kr/ Department of Biomedical Engineering, Hankuk University of Foreign Studies], Korea <br />
**Jonghoon Lee (2013.10-2014.2), currently Assistant Professor, [http://fsb.cha.ac.kr/ Department of Food Science and Biotechnology, CHA University], Korea <br />
<br />
*Former Graduate Students (PhD)<br />
**Junha Shin (2008.9-2014.2), PhD; currently Postdoc Fellow, University of Wisconsin-Madison, USA [https://roylab.discovery.wisc.edu/ Roy Lab]<br />
**Hanhae Kim (2008.9-2015.2), PhD; currently Associate Research Fellow, [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)]<br />
**Ara Cho (2008.9-2015.2), PhD;<br />
**Eiru Kim (2010.9-2016.8), PhD; currently Postdoc Fellow, MD Anderson Cancer Center, Texas, USA [http://www.hart-lab.org/ Hart Lab]<br />
**Tak Lee (2011.3-2017.2), PhD; currently Postdoc Fellow, Yonsei University, Korea<br />
<br />
*Former Graduate Students (Master)<br />
**Sun-Gou Ji (2009.9-2011.8), M.Eng.; PhD from University of Cambrideg (Sanger Genome center); currently R&D engineer at [https://www.sbgenomics.com/ Seven Bridges], USA<br />
**Hyojin Kim (2013.3-2015.2), M.Eng.; currently Bioinformatics Scientist, Aachen University, Germany <br />
**Hongseok Shim (2013.9-2015.8), M.Eng.; <br />
**Sunmo Yang (2014.9-2017.2), M.Eng. currently Bioinformatics programmer, Yonsei University, Korea<br />
<br />
*Former Visiting Scientists/Students<br />
**Minkyung Shin (2012.3-2012.7), went to a graduate school, University of Southern California, USA<br />
**Paul Chung (2012 summer high school student intern), went to University of Pennsylvania; currently E-Commerce Analyst/Coordinator at [http://www.riotgames.com/ Riot Games], USA<br />
**Susie Shin (2013 summer high school student intern), went to Vanderbilt University, USA<br />
**Hyunjin Cho (Johns Hopkins University, Bioinformatics), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA<br />
<br />
*Former Undergraduate Students<br />
**Ila Shin, went to a medical school (Yonsei Univ.)<br />
**Yoonkyung Ko<br />
**Sangyo Park, went to a law school (Kyounghee Univ.)<br />
**Jayoon Shin, went to a medical school (Pusan National Univ.)<br />
**Dongjoo Sun, went to a dental school (Wongwang Univ.)<br />
**Eulsoo Kim<br />
**Myungwhan Lee, went to a medical school (Yonsei Univ.)<br />
**Moonhee Lee, went to a graduate school, University of Amsterdam, Netherlands<br />
**Jinhyun Ju, went to a graduate school, Cornell Medical School, NY, USA (Research field: Computational Systems Biology)<br />
**Haeyoung Shin, went to a graduate school, Brown University, USA (Research field: Computational Neuroscience)<br />
**Joonghee Soh, went to a graduate school, KAIST, Korea (Research field: Culture Technology)<br />
**Hee Jung Cho, went to a graduate school, UC Berkeley <br />
**TaeHwan Kim, went to a medical school<br />
**Joohyung Kim, went to a medical school (Kyungpook National Univ.)<br />
**Donghyun Shin, went to a medical school (Yonsei Univ.)<br />
**Sunphil Kim<br />
**Jaeho Shim<br />
**Seunghyun Shin<br />
**Aejoo Hong<br />
**Changbae Bang<br />
**Seoyoung Choi<br />
**Dabin Jung<br />
**Byunghee Kang<br />
**Borem Nam<br />
**Seungun Lee</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Welcome_to_Network_Biology_Laboratory&diff=4262
Welcome to Network Biology Laboratory
2017-02-16T05:41:35Z
<p>Hhj6212: /* Oral Presentation */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
|rowspan="2" style="padding-right:20px;"|<br />
[[File :groupphoto_20161208_crop.jpg|580px|center|middle|Main Photo]]<br />
<br />
|colspan=2|<br />
=== Research Keyword Cloud (2012-2016)===<br />
<div>{{#widget:AddHtml|content=<img src="../wiki/cloud2.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div><br />
|-<br />
|<br />
<br />
=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| JE Shim<br />
|style="width:65px"| T Lee<br />
|style="width:65px"| HJ Han<br />
|-<br />
| KS Kim<br />
| CY Kim<br />
| DS Bae *<br />
|-<br />
| SM Yang<br />
| MY Lee<br />
| JW Cho<br />
|-<br />
| EB Kim<br />
| SH Lee<br />
|<br />
|}<br />
|<br />
<br />
=== Visitors Trend ===<br />
[https://www.clustrmaps.com/map/Netbiolab.org https://www.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]<br />
|-<br />
|colspan=3|<br />
===Contact Informations===<br />
<pre><br />
Yonsei University <br />
50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea <br />
Science Research Center S323 (Lab) S328 (Professor's Office)<br />
+82-70-8625-5205 <br />
</pre><br />
|}</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Teaching&diff=4261
Teaching
2017-02-16T05:40:08Z
<p>Hhj6212: </p>
<hr />
<div>[[Teaching Materials for Students]]<br />
<br />
[https://www.netbiolab.org/wiki/images/7/7b/2017_BIML_0216_2.zip BIML2017 practice 2 PPT file & python scripts]<br />
<br />
[http://www.netbiolab.org/wiki/images/4/4b/Practice1.pdf BIML2016 practice 1 PPT file]<br />
<br />
[http://www.netbiolab.org/wiki/images/c/c0/Biml_python_scripts.zip BIML2016 practice 2 python scripts]</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=File:2017_BIML_0216_2.zip&diff=4260
File:2017 BIML 0216 2.zip
2017-02-16T05:38:52Z
<p>Hhj6212: </p>
<hr />
<div></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=4226
Journal Club
2017-01-19T01:16:25Z
<p>Hhj6212: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2017<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=1|2017/02/28<br />
|style="padding:.4em;"|2017-11<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[https://www.ncbi.nlm.nih.gov/pubmed/27851969 Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2017/02/21<br />
|style="padding:.4em;"|2017-10<br />
|style="padding:.4em;"|EB Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://biorxiv.org/content/early/2016/12/30/097451 Convergence of dispersed regulatory mutations predicts driver genes in prostate cancer.]<br />
|-<br />
|style="padding:.4em;"|2017-09<br />
|style="padding:.4em;"|EB Kim<br />
|style="padding:.4em;text-align:left"|<br />
[https://www.ncbi.nlm.nih.gov/pubmed/27723759 Chromatin structure-based prediction of recurrent noncoding mutations in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2017/02/14<br />
|style="padding:.4em;"|2017-08<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://biorxiv.org/content/early/2016/11/17/088286 Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2017/02/07<br />
|style="padding:.4em;"|2017-07<br />
|style="padding:.4em;"|MY Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://biorxiv.org/content/early/2016/11/28/090134 Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2017/01/31<br />
|style="padding:.4em;"|2017-06<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[https://www.ncbi.nlm.nih.gov/pubmed/27912059 Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2017/01/24<br />
|style="padding:.4em;"|2017-05<br />
|style="padding:.4em;"|JW Cho<br />
|style="padding:.4em;text-align:left"|<br />
[https://www.ncbi.nlm.nih.gov/pubmed/27851914 Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2017/01/17<br />
|style="padding:.4em;"|2017-04<br />
|style="padding:.4em;"|HJ Han <br />
|style="padding:.4em;text-align:left"|<br />
[https://www.ncbi.nlm.nih.gov/pubmed/25938943 Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C]<br />
|-<br />
|style="padding:.4em;"| 2017-03<br />
|style="padding:.4em;"|EB Kim <br />
|style="padding:.4em;text-align:left"|<br />
[https://www.ncbi.nlm.nih.gov/pubmed/27306882 CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2017/01/10<br />
|style="padding:.4em;"|2017-02<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[https://www.ncbi.nlm.nih.gov/pubmed/26527291 ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2017/01/03<br />
|style="padding:.4em;"|2017-01<br />
|style="padding:.4em;"|SH Lee<br />
|style="padding:.4em;text-align:left"|<br />
[https://www.ncbi.nlm.nih.gov/pubmed/26287467 Single-cell messenger RNA sequencing reveals rare intestinal cell types]<br />
|-<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/12/27<br />
|style="padding:.4em;"|2016-31<br />
|style="padding:.4em;"|EB Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25664528 Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/12/6<br />
|style="padding:.4em;"|2016-30<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26299571 Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/11/29<br />
|style="padding:.4em;"|2016-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24658644 The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/11/22<br />
|style="padding:.4em;"|2016-28<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26887813 Classification of low quality cells from single-cell RNA-seq data.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/11/15<br />
|style="padding:.4em;"|2016-27<br />
|style="padding:.4em;"|MY Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26000487 Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/11/8<br />
|style="padding:.4em;"|2016-26<br />
|style="padding:.4em;"|JW Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26000488 Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/11/1<br />
|style="padding:.4em;"|2016-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27426982 Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/10/25<br />
|style="padding:.4em;"|2016-24<br />
|style="padding:.4em;"|MY Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27549193 Comprehensive analyses of tumor immunity: implications for cancer immunotherapy.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/10/11<br />
|style="padding:.4em;"|2016-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=sidespread+parainflammation Widespread parainflammation in human cancer]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/27<br />
|style="padding:.4em;"|2016-22<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27535533 Analysis of protein-coding genetic variation in 60,706 humans]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/20<br />
|style="padding:.4em;"|2016-21<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
Functional characterization of somatic mutations in cancer using network-based inference of protein activity<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27322546 pubmed]<br />
[http://www.nature.com/ng/journal/v48/n8/full/ng.3593.html fulltext]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/13<br />
|style="padding:.4em;"|2016-20<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=exploiting+single-cell+expression+to+characterize Exploiting single-cell expression to characterize co-expression replicability.]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/9/6<br />
|style="padding:.4em;"|2016-19<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26940869 Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/31<br />
|style="padding:.4em;"|2016-18<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27264179 A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/16<br />
|style="padding:.4em;"|2016-17<br />
|style="padding:.4em;"|JW Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27309802 The landscape of accessible chromatin in mammalian preimplantation embryos]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/8<br />
|style="padding:.4em;"|2016-16<br />
|style="padding:.4em;"|EB Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27064255 Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/8/1<br />
|style="padding:.4em;"|2016-15<br />
|style="padding:.4em;"|MY Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27040498 Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/25<br />
|style="padding:.4em;"|2016-14<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=integration+of+summary+data+from+gwas+and+eqtl+studies Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2016/7/18<br />
|style="padding:.4em;"|2016-13<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23624555 Identification of transcriptional regulators in the mouse immune system]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
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|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
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|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
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|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
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|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
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|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
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|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
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|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
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|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
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|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
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|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
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|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
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|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
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|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
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[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
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|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
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|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
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|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
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|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
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|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
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|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
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|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
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|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
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|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
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|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=People&diff=3901
People
2016-06-30T05:22:44Z
<p>Hhj6212: /* Graduate Students */</p>
<hr />
<div>__NOTOC__<br />
=='''Principal Investigator'''==<br />
{|border="0" width="150"<br />
|align="center"|[[File:People_ISLee_03.jpg|77px|link=people:IS_Lee]]<br />
|-<br />
|align="center"|[[people:IS_Lee|Insuk Lee]]<br />
|-<br />
|}<br />
<br />
=='''Research Professor/Postdoc Fellow/Staff Scientist'''==<br />
{|border="0" width="300"<br />
|align="center"|[[File:People_JE_Shim_EDIT.JPG|70px|link=people:JE_Shim]]<br />
|align="center"|[[File:SYLee.jpg|70px|link=people:SY_Lee]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Jung Eun Shim]]<br />
|align="center"|[[people:SY_Lee|Sangyoung Lee]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Research Professor]]<br />
|align="center"|[[people:SY_Lee|Research Assistant]]<br />
|}<br />
<br />
=='''Graduate Students'''==<br />
{|border="0" width="1000"<br />
|align="center" |[[File:Banmyungham.JPG|70px|link=people:ER_Kim]]<br />
|align="center" |[[File:Tak_sajin3.jpg|70px|link=people:T_Lee]]<br />
|align="center" |[[File:heonjong.jpg|70px|link=people:HJ_Han]]<br />
|align="center" |[[File:People_KSKim.jpg|70px|link=people:KS_Kim]]<br />
|align="center"|[[File:Smyang.jpg|70px|link=people:SM_Yang]]<br />
|align="center"|[[File:배다솜.jpg|70px|link=People:DS Bae]]<br />
|align="center"|[[File:CY KIM.jpg|70px|link=People:CY_Kim]]<br />
|align="center"|[[File:Muyoung_Lee_2.jpg|70px|link=People:M_Lee]]<br />
|align="center"|[[File:Cho_JW.png|70px|link=People:J_Cho]]<br />
|align="center"|[[File:kim_EB.jpg|70px|link=People:E_Kim]]<br />
|-<br />
|align="center"|[[people:ER_Kim|Eiru Kim]]<br />
|align="center"|[[people:T_Lee|Tak Lee]]<br />
|align="center"|[[people:HJ_Han|Heon Jong Han]]<br />
|align="center"|[[people:KS_Kim|Kyungsoo Kim]]<br />
|align="center"|[[people:SM_Yang|Sunmo Yang]]<br />
|align="center"|[[People:DS Bae|Dasom Bae]]<br />
|align="center"|[[People:CY Kim|Chan Yeong Kim]]<br />
|align="center"|[[People:M_Lee|Muyoung Lee]]<br />
|align="center"|[[People:J_Cho|Jaewan Cho]]<br />
|align="center"|[[People:E_Kim|Eunbeen Kim]]<br />
|-<br />
|align="center"|[[people:ER_Kim|PhD candidate]]<br />
|align="center"|[[people:T_Lee|PhD candidate]]<br />
|align="center"|[[People:HJ_Han|PhD course]]<br />
|align="center"|[[people:KS_Kim|PhD course]]<br />
|align="center"|[[people:SM_Yang|M.Eng. course/System Admin]]<br />
|align="center"|[[people:DS Bae|PhD course]]<br />
|align="center"|[[people:CY Kim|PhD course]]<br />
|align="center"|[[people:M_Lee|PhD course]]<br />
|align="center"|[[people:J_Cho|PhD course]]<br />
|align="center"|[[people:E_Kim|PhD course]]<br />
|}<br />
<br />
=='''Undergraduate Students'''==<br />
<br />
<br />
=='''Visiting scientists/students'''==<br />
<br />
<br />
=='''Alumni'''==<br />
*Former Post-docs and Staff Scientists<br />
**Taeyun Oh (2009.5-2011.12), current position: Deputy Principal Consultant, INSILICOGEN (www.insilicogen.com) <br />
**Samuel Beck (2011.2-2011.12), current position; Postdoc fellow, University of Texas at Austin [http://web.biosci.utexas.edu/kimlab/ Jonghwan Kim's Lab]<br />
**Jawon Song (2011.1-2012.5), current position; Research Scientist, Texas Advanced Computing Center, Austin, TX, USA<br />
**Yoonhee Ko (2012.8-2014.2), current position; Fellow, Severance Medical center (Yonsei Medical school)<br />
**Jonghoon Lee (2013.10-2014.2), current position; Assistant Professor, CHA Medical school <br />
**Sohyun Hwang (2010.3-2015.8), current position; Research Professor, Ewha Womans University<br />
<br />
*Former Graduate Students<br />
**Sungou Ji (2009.9-2011.8), M.Eng.; current position; Postdoc fellow, Sanger Genome Institute, Cambridge University, UK (Research field: Statistical Genomics)<br />
**Junha Shin (2008.9-2014.2), PhD; <br />
**Hanhae Kim (2008.9-2015.2), PhD; current position; Associate Research Fellow, Korea Institute of S&T Evaluation and Planning (KISTEP)<br />
**Ara Cho (2008.9-2015.2), PhD; <br />
**Hyojin Kim (2013.3-2015.2), M.Eng.; current position; Research Assistant, Samsung Advanced Institute for Health Sciences & Technology (SAIHST)<br />
**Hongseok Shim (2013.9-2015.8), M.Eng.; <br />
<br />
*Former Visiting Scientists/Students<br />
**Minkyung Shin (2012.3-2012.7), went to a graduate school, University of Southern California, USA<br />
**Paul Chung (2012 summer high school student intern), went to University of Pennsylvania (Bio Engineering) <br />
**Susie Shin (2013 summer high school student intern), went to Vanderbilt University (Bio Engineering)<br />
**Hyunjin Cho (Johns Hopkins University, Bioinformatics)<br />
<br />
*Former Undergraduate Students<br />
**Ila Shin, went to a medical school (Yonsei Univ.)<br />
**Yoonkyung Ko<br />
**Sangyo Park, went to a law school (Kyounghee Univ.)<br />
**Jayoon Shin, went to a medical school (Pusan National Univ.)<br />
**Dongjoo Sun, went to a dental school (Wongwang Univ.)<br />
**Eulsoo Kim<br />
**Myungwhan Lee, went to a medical school (Yonsei Univ.)<br />
**Moonhee Lee, went to a graduate school, University of Amsterdam, Netherlands<br />
**Jinhyun Ju, went to a graduate school, Cornell Medical School, NY, USA (Research field: Computational Systems Biology)<br />
**Haeyoung Shin, went to a graduate school, Brown University, USA (Research field: Computational Neuroscience)<br />
**Joonghee Soh, went to a graduate school, KAIST, Korea (Research field: Culture Technology)<br />
**Hee Jung Cho, went to a graduate school, UC Berkeley <br />
**TaeHwan Kim, went to a medical school<br />
**Joohyung Kim, went to a medical school (Kyungpook National Univ.)<br />
**Donghyun Shin, went to a medical school (Yonsei Univ.)<br />
**Sunphil Kim<br />
**Jaeho Shim<br />
**Seunghyun Shin</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Services&diff=3530
Services
2015-05-26T01:29:45Z
<p>Hhj6212: </p>
<hr />
<div>__NOTOC__<br />
=='''Genome-scale functional gene networks'''==<br />
==''Animal''==<br />
{|border="0" width="600"<br />
|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]<br />
|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]<br />
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]<br />
|-<br />
|align="center"|''Caenorhabditis elegans''<br />
|align="center"|''Drosophila melanogaster''<br />
|align="center"|''Homo sapiens''<br />
|}<br />
==''Plant''==<br />
{|border="0" width="400"<br />
|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]]<br />
|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]<br />
|-<br />
|align="center"|''Arabidopsis thaliana''<br />
|align="center"|''Oryza sativa''<br />
|}<br />
==''Microbe''==<br />
{|border="0" width="600"<br />
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]<br />
|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]]<br />
|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]]<br />
|-<br />
|align="center"|''Escherichia coli''<br />
|align="center"|''Saccharomyces cerevisiae''<br />
|align="center"|''Cryptococcus neoformans''<br />
|}<br />
<br />
=='''RIDDLE: for network-assisted Gene Set Analysis'''==<br />
[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] RIDDLE (Reflective diffusion and local extension) is currently available for only human genes.<br />
=='''MORPHIN: to study human diseases based on model organism pathways'''==<br />
[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] Morphin (Model Organisms Projected on a Human Integrated Gene Network) is currently available.<br />
=='''JiffyNet: to construct gene network for newly sequenced species'''==<br />
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]] Jiffy (instant) gene network modeler for newly sequenced species</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=People:Album:2015_Teachers%27_day&diff=3526
People:Album:2015 Teachers' day
2015-05-15T08:33:38Z
<p>Hhj6212: </p>
<hr />
<div><gallery><br />
File:2015teachersday1.jpg<br />
File:2015teachersday2.jpg<br />
File:2015teachersday3.jpg<br />
</gallery></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=People:Album:2015_Teachers%27_day&diff=3525
People:Album:2015 Teachers' day
2015-05-15T08:33:16Z
<p>Hhj6212: Created page with "File:2015teachersday1.jpg File:2015teachersday2.jpg File:2015teachersday3.jpg"</p>
<hr />
<div>File:2015teachersday1.jpg<br />
File:2015teachersday2.jpg<br />
File:2015teachersday3.jpg</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Album&diff=3524
Album
2015-05-15T08:32:56Z
<p>Hhj6212: </p>
<hr />
<div>__NOTOC__<br />
=='''Group Photo'''==<br />
{|border="0" width="500"<br />
|<br />
[[File:2014group3.JPG|thumb|2014]]<br />
|align="center"|<br />
[[File:2013단체1.jpg|thumb|2013]]<br />
|align="center"|<br />
[[File:People_Album_Spring2012_main.jpg|thumb|2012]]<br />
|-<br />
|align="center"|<br />
[[File:People_Album_Spring2011_05.jpg|thumb|2011]]<br />
|align="center" |<br />
[[File:People_Album_Spring2010_01.jpg|thumb|2010]]<br />
|}<br />
----<br />
*[[People:Album:2015 Teachers' day | 2015 Teacher's day]]<br />
----<br />
*[[People:Album:2014 Summer MT | 2014 Summer MT]]<br />
----<br />
*[[People:Album:2014 Group photo | 2014 Group photo]]<br />
----<br />
*[[People:Album:2013 Summer MT | 2013 Summer MT]]<br />
----<br />
*[[People:Album:2013 Group photo | 2013 Group photo]]<br />
----<br />
*[[People:Album:Teachers' day 2013| 2013 May, Teachers' day]]<br />
----<br />
*[[People:Album:ThanksGivingDay_2012| 2012 Nov, Thanksgiving Day]]<br />
----<br />
*[[People:Album:MT_2012| 2012 June, Summer MT]]<br />
----<br />
*[[People:Album:GroupPhoto_2012_Spring|2012 April, Group Photo]]<br />
----<br />
*[[People:Album:Keystone_2012| 2012 February, Keystone]]<br />
----<br />
*[[People:Album:MT_2011| 2011 August, Summer MT]]<br />
----<br />
*[[People:Album:ISSCR_2011| 2011 June, ISSCR]]<br />
----<br />
*[[People:Album:RECOMB_2011| 2011 March, RECOMB2011]]<br />
----<br />
*[[People:Album:AYRCOB5th_2011| 2011 August, Ayrcob 5th]]<br />
----<br />
*[[People:Album:Teachers_Day_2011| 2011 May, Teacher's day]]<br />
----<br />
*[[People:Album:GroupPhoto_2011_Spring|2011 March, Group Photo]]<br />
----<br />
*[[People:Album:APBC2011|2011 February, APBC (Incheon)]]<br />
----<br />
*[[People:Album:ISMB2010|2010 June, ISMB(Boston)]]<br />
----<br />
*[[People:Album:Sue2010|2010 June, Sue Rhee visit]]<br />
----<br />
*[[People:Album:Cup_cake_2010| 2010 May, Cup Cake professor]]<br />
----<br />
*[[People:Album:Edward_Marcotte_at_NBL|2010 May, Edward Marcotte and @NBL Reunion]]<br />
----<br />
*[[People:Album:GroupPhoto_2010_Spring|2010 March, Group Photo]]<br />
----<br />
*[[People:Album:KSBSB2009|2009 November, KSBSB (Pusan)]]<br />
----<br />
*[[People:Album:ICSB2009|2009 August, ICSB (Stanford)]]<br />
----<br />
*[[People:Album:winter_MT_2008|2008 December, Winter MT]]</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=File:2015teachersday1.jpg&diff=3523
File:2015teachersday1.jpg
2015-05-15T08:32:32Z
<p>Hhj6212: </p>
<hr />
<div></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=People:Album:2015_Teacher%27s_day&diff=3522
People:Album:2015 Teacher's day
2015-05-15T08:31:46Z
<p>Hhj6212: </p>
<hr />
<div><gallery><br />
File:2015teachersday1.jpg<br />
File:2015teachersday2.jpg<br />
File:2015teachersday3.jpg<br />
</gallery></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=File:2015teachersday3.jpg&diff=3521
File:2015teachersday3.jpg
2015-05-15T08:31:22Z
<p>Hhj6212: </p>
<hr />
<div></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=File:2015teachersday2.jpg&diff=3520
File:2015teachersday2.jpg
2015-05-15T08:30:36Z
<p>Hhj6212: </p>
<hr />
<div></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=People:Album:2015_Teacher%27s_day&diff=3517
People:Album:2015 Teacher's day
2015-05-15T08:22:52Z
<p>Hhj6212: Created page with "<gallery> File:2014summermt1.jpg File:2014summermt2.jpg </gallery>"</p>
<hr />
<div><gallery><br />
File:2014summermt1.jpg<br />
File:2014summermt2.jpg<br />
</gallery></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Album&diff=3516
Album
2015-05-15T08:22:34Z
<p>Hhj6212: </p>
<hr />
<div>__NOTOC__<br />
=='''Group Photo'''==<br />
{|border="0" width="500"<br />
|<br />
[[File:2014group3.JPG|thumb|2014]]<br />
|align="center"|<br />
[[File:2013단체1.jpg|thumb|2013]]<br />
|align="center"|<br />
[[File:People_Album_Spring2012_main.jpg|thumb|2012]]<br />
|-<br />
|align="center"|<br />
[[File:People_Album_Spring2011_05.jpg|thumb|2011]]<br />
|align="center" |<br />
[[File:People_Album_Spring2010_01.jpg|thumb|2010]]<br />
|}<br />
----<br />
*[[People:Album:2015 Teacher's day | 2015 Teacher's day]]<br />
----<br />
*[[People:Album:2014 Summer MT | 2014 Summer MT]]<br />
----<br />
*[[People:Album:2014 Group photo | 2014 Group photo]]<br />
----<br />
*[[People:Album:2013 Summer MT | 2013 Summer MT]]<br />
----<br />
*[[People:Album:2013 Group photo | 2013 Group photo]]<br />
----<br />
*[[People:Album:Teachers' day 2013| 2013 May, Teachers' day]]<br />
----<br />
*[[People:Album:ThanksGivingDay_2012| 2012 Nov, Thanksgiving Day]]<br />
----<br />
*[[People:Album:MT_2012| 2012 June, Summer MT]]<br />
----<br />
*[[People:Album:GroupPhoto_2012_Spring|2012 April, Group Photo]]<br />
----<br />
*[[People:Album:Keystone_2012| 2012 February, Keystone]]<br />
----<br />
*[[People:Album:MT_2011| 2011 August, Summer MT]]<br />
----<br />
*[[People:Album:ISSCR_2011| 2011 June, ISSCR]]<br />
----<br />
*[[People:Album:RECOMB_2011| 2011 March, RECOMB2011]]<br />
----<br />
*[[People:Album:AYRCOB5th_2011| 2011 August, Ayrcob 5th]]<br />
----<br />
*[[People:Album:Teachers_Day_2011| 2011 May, Teacher's day]]<br />
----<br />
*[[People:Album:GroupPhoto_2011_Spring|2011 March, Group Photo]]<br />
----<br />
*[[People:Album:APBC2011|2011 February, APBC (Incheon)]]<br />
----<br />
*[[People:Album:ISMB2010|2010 June, ISMB(Boston)]]<br />
----<br />
*[[People:Album:Sue2010|2010 June, Sue Rhee visit]]<br />
----<br />
*[[People:Album:Cup_cake_2010| 2010 May, Cup Cake professor]]<br />
----<br />
*[[People:Album:Edward_Marcotte_at_NBL|2010 May, Edward Marcotte and @NBL Reunion]]<br />
----<br />
*[[People:Album:GroupPhoto_2010_Spring|2010 March, Group Photo]]<br />
----<br />
*[[People:Album:KSBSB2009|2009 November, KSBSB (Pusan)]]<br />
----<br />
*[[People:Album:ICSB2009|2009 August, ICSB (Stanford)]]<br />
----<br />
*[[People:Album:winter_MT_2008|2008 December, Winter MT]]</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=File:2015nblexperiment.zip&diff=3499
File:2015nblexperiment.zip
2015-04-15T01:00:07Z
<p>Hhj6212: Hhj6212 uploaded a new version of &quot;File:2015nblexperiment.zip&quot;</p>
<hr />
<div></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=File:2015nblexperiment.zip&diff=3491
File:2015nblexperiment.zip
2015-04-10T08:37:39Z
<p>Hhj6212: Hhj6212 uploaded a new version of &quot;File:2015nblexperiment.zip&quot;</p>
<hr />
<div></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Teaching_Materials_for_Students&diff=3490
Teaching Materials for Students
2015-04-10T08:22:44Z
<p>Hhj6212: </p>
<hr />
<div>[http://www.netbiolab.org/wiki/images/2/2c/2015nblexperiment.zip 2015 netbiolab experiment sample]<br />
<br />
[http://www.netbiolab.org/wiki/images/9/91/2014NetbioSampleNetwork.zip 2014 netbiolab experiment sample]<br />
<br />
[http://www.netbiolab.org/wiki/images/4/4c/LAB6_instructions.pdf experiment demonstration file]</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Teaching_Materials_for_Students&diff=3489
Teaching Materials for Students
2015-04-10T08:18:25Z
<p>Hhj6212: </p>
<hr />
<div>[http://www.netbiolab.org/wiki/images/9/91/2014NetbioSampleNetwork.zip 2014 netbiolab experiment sample]<br />
<br />
[http://www.netbiolab.org/wiki/images/4/4c/LAB6_instructions.pdf experiment demonstration file]</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Teaching_Materials_for_Students&diff=3488
Teaching Materials for Students
2015-04-10T08:18:12Z
<p>Hhj6212: </p>
<hr />
<div>[[File:2015nblexperiment.zip|thumbnail]]<br />
2015 netbiolab experiment sample]<br />
<br />
[http://www.netbiolab.org/wiki/images/9/91/2014NetbioSampleNetwork.zip 2014 netbiolab experiment sample]<br />
<br />
[http://www.netbiolab.org/wiki/images/4/4c/LAB6_instructions.pdf experiment demonstration file]</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Teaching_Materials_for_Students&diff=3487
Teaching Materials for Students
2015-04-10T08:15:05Z
<p>Hhj6212: </p>
<hr />
<div>[http://www.netbiolab.org/wiki/images/9/91/2015nblexperiment.zip 2015 netbiolab experiment sample]<br />
<br />
[http://www.netbiolab.org/wiki/images/9/91/2014NetbioSampleNetwork.zip 2014 netbiolab experiment sample]<br />
<br />
[http://www.netbiolab.org/wiki/images/4/4c/LAB6_instructions.pdf experiment demonstration file]</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=File:2015nblexperiment.zip&diff=3486
File:2015nblexperiment.zip
2015-04-10T08:14:49Z
<p>Hhj6212: </p>
<hr />
<div></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Teaching_Materials_for_Students&diff=3485
Teaching Materials for Students
2015-04-10T08:13:03Z
<p>Hhj6212: </p>
<hr />
<div>[http://www.netbiolab.org/wiki/images/9/91/netbiolab_experiment.zip 2015 netbiolab experiment sample]<br />
<br />
[http://www.netbiolab.org/wiki/images/9/91/2014NetbioSampleNetwork.zip 2014 netbiolab experiment sample]<br />
<br />
[http://www.netbiolab.org/wiki/images/4/4c/LAB6_instructions.pdf experiment demonstration file]</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Teaching_Materials_for_Students&diff=3484
Teaching Materials for Students
2015-04-10T08:12:53Z
<p>Hhj6212: </p>
<hr />
<div>[http://www.netbiolab.org/wiki/images/9/91/netbiolab experiment.zip 2015 netbiolab experiment sample]<br />
<br />
[http://www.netbiolab.org/wiki/images/9/91/2014NetbioSampleNetwork.zip 2014 netbiolab experiment sample]<br />
<br />
[http://www.netbiolab.org/wiki/images/4/4c/LAB6_instructions.pdf experiment demonstration file]</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Teaching_Materials_for_Students&diff=3482
Teaching Materials for Students
2015-04-10T08:08:57Z
<p>Hhj6212: </p>
<hr />
<div>[http://www.netbiolab.org/wiki/images/9/91/2015_학부실험.zip 2015 netbiolab experiment sample]<br />
<br />
[http://www.netbiolab.org/wiki/images/9/91/2014NetbioSampleNetwork.zip 2014 netbiolab experiment sample]<br />
<br />
[http://www.netbiolab.org/wiki/images/4/4c/LAB6_instructions.pdf experiment demonstration file]</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3259
Journal Club
2014-07-22T01:33:46Z
<p>Hhj6212: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Welcome_to_Network_Biology_Laboratory&diff=3258
Welcome to Network Biology Laboratory
2014-07-21T04:56:25Z
<p>Hhj6212: /* Oral Presentation */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0"<br />
|rowspan="2"|<br />
[[File :2014group3.JPG|544px|center|middle|Main Photo]]<br />
<br />
|colspan=2|<br />
[http://www2.clustrmaps.com/user/563d3fa7 http://www2.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]<br />
|-<br />
|width="185" style="text-align:center;vertical-align:top;padding:0 0 0 5px;"|<br />
=== Oral Presentation ===<br />
<pre style="text-align:left;"><br />
HH Kim <br />
JE Shim <br />
T Lee <br />
AR Cho <br />
HJ Han **<br />
HS Shim <br />
JH Shin <br />
KS Kim<br />
ER Kim<br />
HJ Kim <br />
CY Kim<br />
DS Bae <br />
BH Kang <br />
</pre><br />
<br />
|-<br />
<br />
|colspan=3|<br />
<br />
===Contact Informations===<br />
<pre><br />
Yonsei University 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea <br />
Office: Engineering Research Park B118DA<br />
<br />
+82-70-8625-5205 <br />
</pre><br />
|}</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3256
Journal Club
2014-07-18T07:34:50Z
<p>Hhj6212: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/29<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
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<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3255
Journal Club
2014-07-18T07:33:43Z
<p>Hhj6212: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/29<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3254
Journal Club
2014-07-18T07:30:51Z
<p>Hhj6212: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/08/12<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/08/12<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/08/05<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/07/29<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3253
Journal Club
2014-07-18T07:28:31Z
<p>Hhj6212: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/08/12<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/08/05<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/07/29<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3252
Journal Club
2014-07-18T07:28:03Z
<p>Hhj6212: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/08/12<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/08/05<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/07/29<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3251
Journal Club
2014-07-18T07:21:59Z
<p>Hhj6212: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/07/29<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Journal_Club&diff=3250
Journal Club
2014-07-18T07:21:12Z
<p>Hhj6212: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/07/29<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Publications&diff=3242
Publications
2014-07-13T03:21:11Z
<p>Hhj6212: /* 2014 */</p>
<hr />
<div>*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report] <br />
{{#widget:AddHtml<br />
|content=<span id='badgeCont967476' style='width:126px'><a title="Insuk Lee's Profile" href='http://www.researcherid.com/rid/F-7722-2010' target='_blank'><img src='http://labs.researcherid.com/mashlets/badge/rid-idsymbol4.gif' border='0'></a></span><br />
}}<br />
<br />
* '*' co-corresponding authorship<br />
==2014==<br />
*37. Hwang S, Kim E, Yang S, Marcotte EM, '''Lee I''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]<br />
*36. '''Lee I''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]<br />
*35. Ara Cho, Junha Shin, Sohyun Hwang, Chanyung Kim, Hongsuk Shim, Hyojin Kim, Hanhae Kim, '''Insuk Lee''', WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 May 9 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]<br />
*34. Junha Shin, Tak Lee, Hanhae Kim and '''Insuk Lee''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 10 (1), 24 - 29., (2014) [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]<br />
*33. Hanhae Kim, Junha Shin, Eiru Kim, Hyojin Kim, Sohyun Hwang, Jung Eun Shim, '''Insuk Lee''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 42 (D1): D731-D736., (2014) [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]<br />
<br />
==2013==<br />
*32. Eiru Kim, Hanhae Kim and '''Insuk Lee''', JiffyNet: a web-based instant protein network modeler for newly sequenced species. '''''Nucleic Acids Research''''' 41 (W1): W192-W197., (2013) [http://www.ncbi.nlm.nih.gov/pubmed/23685435 Pubmed][http://nar.oxfordjournals.org/content/early/2013/05/17/nar.gkt419.full.pdf+html pdf]<br />
*31. '''Insuk Lee''', Network approaches to the genetic dissection of phenotypes in animals and humans. '''''Animal Cells and Systems''''' Vol.17,No.2,75-79(2013)[http://www.tandfonline.com/doi/abs/10.1080/19768354.2013.789076 Link]<br />
<br />
==2012==<br />
*30. Peggy I Wang, Sohyun Hwang, Rodney P Kincaid, Christopher S Sullivan, '''Insuk Lee*''', and Edward M Marcotte*. RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. '''''Genome Biology''''' 13:R125 (2012)[http://www.ncbi.nlm.nih.gov/pubmed/23268829 pubmed] <br />
*29. Lee Chae*, '''Insuk Lee*''', Junha Shin, and Seung Yon Rhee*. Towards understanding how molecular networks evolve in plant. '''''Current Opinion in Plant Biology''''' 15:177-184 (2012)[http://www.ncbi.nlm.nih.gov/pubmed/22280840 pubmed] [[media:CurrOpinPlantBiol 15-177.pdf|pdf]]<br />
*28. Stephanie M. Quanbeck, Libuse Brachova, Alexis A. Campbell, Xin Guan, Ann Perera, Kun He, Seung Y. Rhee, Preeti Bais, Julie A. Dickerson, Philip Dixon, Gert Wohlgemuth, Oliver Fiehn, Lenore Barken, Iris Lange, B. Markus Lange, '''Insuk Lee''', Diego Cortes, Carolina Salazar, Joel Shuman, Vladimir Shulaev, David V. Huhman, Lloyd W. Sumner, Mary R. Roth, Ruth Welti, Hilal Ilarslan, Eve S. Wurtele, and Basil J. Nikolau. Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of “unknown function”. '''''Frontiers in Plant Science''''' 3:1-12 (2012) [http://www.ncbi.nlm.nih.gov/pubmed/22645570/ pubmed][[media:Fpls-03-00015.pdf|pdf]]<br />
<br />
==2011==<br />
*27. '''Insuk Lee*''', Young-Su Seo, Dusica Coltrane, Sohyun Hwang, Taeyun Oh, Edward M. Marcotte*, and Pamela C. Ronald*. Genetic dissection of the biotic stress response using a genome-scale gene network for rice. '''''PNAS''''' 108(45):18548-53 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/22042862 pubmed] [[media:PNAS-2011-Lee-18548-53.pdf|pdf]]<br />
<br />
*26. Sohyun Hwang, Seung Y. Rhee*, Edward M. Marcotte*, and '''Insuk Lee*'''. Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana. '''''Nature Protocols''''' 6:1429-1442 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21886106 pubmed][[media:2011.08.25.online.nprot.2011.372.pdf|pdf]]<br />
<br />
*25. '''Insuk Lee''', Probabilistic functional gene societies. '''''Progress in Biophysics and Molecular Biology''''' 106:435-442 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21281658 pubmed] [[media:Publications_023_n.pdf|pdf]]<br />
<br />
*24. '''Insuk Lee*''', U. Martin Blom, Peggy I. Wang, Jung Eun Shim, and Edward M. Marcotte*. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. '''''Genome Research''''' 21:1109-1121 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21536720 pubmed] [[media:Publications_025_n.pdf|pdf]]<br />
<br />
*23. Young-Su Seo, Mawsheng Chern, Laura E. Bartley, Muho Han, Ki-Hong Jung, '''Insuk Lee''', Harkamal Walia, Todd Richter, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E. Canlas, Randy Ruan, Chang-Jin Park, Xuewel Chen, Sohyun Hwang, Jong-Seong Jeon, and Pamela C. Ronald. Towards establishment of a rice stress response interactome. '''''PLoS Genetics''''' 7(4):e1002020 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21533176 pubmed] [[media:Publications_024.pdf|pdf]]<br />
<br />
==2010==<br />
*22. Ni Huang, '''Insuk Lee''', Edward M.Marcotte, Matthew E.Hurles, Characterising and predicting haploinsufficiency in the human genome, '''''PLoS Genet.''''' 6(10):e1001154(2010) [http://www.ncbi.nlm.nih.gov/pubmed/20976243 pubmed] [[media:Publications_022.pdf|pdf]]<br />
<br />
*21. Eiru Kim, Jaeyoon Shin and '''Insuk Lee''', Assessment of effectiveness of the network-guided genetic screen, '''''Mol Biosyst.''''' 6:1803-1806(2010) [http://www.ncbi.nlm.nih.gov/pubmed/20697632 pubmed] [[media:Publications_021.pdf|pdf]]<br />
<br />
*20. '''Insuk Lee*''', Ben Lehner, Tanya Vavouri, Junha Shin, Andrew G. Fraser, and Edward M. Marcotte, Predicting genetic modifier loci using functional gene networks, '''''Genome Research''''', 20:1143-1153(2010) . co-corresponding author [http://www.ncbi.nlm.nih.gov/pubmed/20538624 pubmed] [[media:Publications_020.pdf|pdf]]<br />
<br />
*19. '''Insuk Lee*''', Bindu Ambaru, Pranjali Thakkar, Edward M Marcotte*, Seung Y Rhee*, Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana, '''''Nature Biotechnology''''', 28:149-156 (2010). ''co-corresponding author'' [http://www.ncbi.nlm.nih.gov/pubmed/20118918 pubmed] [[media:Publications_019.pdf|pdf]]<br />
==2009==<br />
*18. '''Insuk Lee''' and Edward Marcotte. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. p463-475 (2009) [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]<br />
<br />
*17. Zhihua Li, '''Insuk Lee''', Emily Moradi, Nai-Jung Hung, Arlen W. Johnson, Edward M. Marcotte, Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 7(10):e1000213 (2009) [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]<br />
<br />
*16. Ryan S. Gray, Philip B. Abitua, Bogdan J. Wlodarczyk, Heather L. Szabo-Rogers, Otis Blanchard, '''Insuk Lee''', Greg S. Weiss, Karen J. Liu, Edward M. Marcotte, John B. Wallingford, Richard H. Finnell. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 11:1225-32 (2009) '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]<br />
==2008==<br />
*15. Ben Lehner* and '''Insuk Lee*'''. Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 7:217-227 (2008). '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]<br />
<br />
*14. '''Insuk Lee''' and Edward Marcotte. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. p267-278 (2008) [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]<br />
<br />
*13. '''Insuk Lee''', Ben Lehner, Catriona Crombie, Wendy Wong, Andrew G. Fraser, Edward M. Marcotte. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 40:181-188 (2008). '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]]<br />This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)<br />
<br />
==Before 2007==<br />
*12. '''Insuk Lee''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]<br />
<br />
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]<br />
<br />
*10. '''Insuk Lee''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]<br />
<br />
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]<br />
<br />
*8. Insuk Lee, Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]<br />
<br />
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]<br />
<br />
*6. '''Insuk Lee''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)<br />
<br />
*5. '''Insuk Lee''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)<br />
<br />
*4. '''Insuk Lee''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)<br />
<br />
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)<br />
<br />
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998) <br />
<br />
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)<br />
==Patent==<br />
*[https://www.google.com/patents/WO2013055867A1?cl=en&dq=ininventor:%22Insuk+LEE%22&hl=en&sa=X&ei=owFiU5XqMM-B8gXP3YFw&ved=0CDcQ6AEwAA Genes involved in stress response in plants]</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Publications&diff=3241
Publications
2014-07-13T03:21:01Z
<p>Hhj6212: /* 2014 */</p>
<hr />
<div>*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report] <br />
{{#widget:AddHtml<br />
|content=<span id='badgeCont967476' style='width:126px'><a title="Insuk Lee's Profile" href='http://www.researcherid.com/rid/F-7722-2010' target='_blank'><img src='http://labs.researcherid.com/mashlets/badge/rid-idsymbol4.gif' border='0'></a></span><br />
}}<br />
<br />
* '*' co-corresponding authorship<br />
==2014==<br />
*37. Hwang S, Kim E, Yang S, Marcotte EM, '''Lee I''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53.[http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]<br />
*36. '''Lee I''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]<br />
*35. Ara Cho, Junha Shin, Sohyun Hwang, Chanyung Kim, Hongsuk Shim, Hyojin Kim, Hanhae Kim, '''Insuk Lee''', WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 May 9 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]<br />
*34. Junha Shin, Tak Lee, Hanhae Kim and '''Insuk Lee''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 10 (1), 24 - 29., (2014) [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]<br />
*33. Hanhae Kim, Junha Shin, Eiru Kim, Hyojin Kim, Sohyun Hwang, Jung Eun Shim, '''Insuk Lee''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 42 (D1): D731-D736., (2014) [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]<br />
<br />
==2013==<br />
*32. Eiru Kim, Hanhae Kim and '''Insuk Lee''', JiffyNet: a web-based instant protein network modeler for newly sequenced species. '''''Nucleic Acids Research''''' 41 (W1): W192-W197., (2013) [http://www.ncbi.nlm.nih.gov/pubmed/23685435 Pubmed][http://nar.oxfordjournals.org/content/early/2013/05/17/nar.gkt419.full.pdf+html pdf]<br />
*31. '''Insuk Lee''', Network approaches to the genetic dissection of phenotypes in animals and humans. '''''Animal Cells and Systems''''' Vol.17,No.2,75-79(2013)[http://www.tandfonline.com/doi/abs/10.1080/19768354.2013.789076 Link]<br />
<br />
==2012==<br />
*30. Peggy I Wang, Sohyun Hwang, Rodney P Kincaid, Christopher S Sullivan, '''Insuk Lee*''', and Edward M Marcotte*. RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. '''''Genome Biology''''' 13:R125 (2012)[http://www.ncbi.nlm.nih.gov/pubmed/23268829 pubmed] <br />
*29. Lee Chae*, '''Insuk Lee*''', Junha Shin, and Seung Yon Rhee*. Towards understanding how molecular networks evolve in plant. '''''Current Opinion in Plant Biology''''' 15:177-184 (2012)[http://www.ncbi.nlm.nih.gov/pubmed/22280840 pubmed] [[media:CurrOpinPlantBiol 15-177.pdf|pdf]]<br />
*28. Stephanie M. Quanbeck, Libuse Brachova, Alexis A. Campbell, Xin Guan, Ann Perera, Kun He, Seung Y. Rhee, Preeti Bais, Julie A. Dickerson, Philip Dixon, Gert Wohlgemuth, Oliver Fiehn, Lenore Barken, Iris Lange, B. Markus Lange, '''Insuk Lee''', Diego Cortes, Carolina Salazar, Joel Shuman, Vladimir Shulaev, David V. Huhman, Lloyd W. Sumner, Mary R. Roth, Ruth Welti, Hilal Ilarslan, Eve S. Wurtele, and Basil J. Nikolau. Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of “unknown function”. '''''Frontiers in Plant Science''''' 3:1-12 (2012) [http://www.ncbi.nlm.nih.gov/pubmed/22645570/ pubmed][[media:Fpls-03-00015.pdf|pdf]]<br />
<br />
==2011==<br />
*27. '''Insuk Lee*''', Young-Su Seo, Dusica Coltrane, Sohyun Hwang, Taeyun Oh, Edward M. Marcotte*, and Pamela C. Ronald*. Genetic dissection of the biotic stress response using a genome-scale gene network for rice. '''''PNAS''''' 108(45):18548-53 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/22042862 pubmed] [[media:PNAS-2011-Lee-18548-53.pdf|pdf]]<br />
<br />
*26. Sohyun Hwang, Seung Y. Rhee*, Edward M. Marcotte*, and '''Insuk Lee*'''. Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana. '''''Nature Protocols''''' 6:1429-1442 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21886106 pubmed][[media:2011.08.25.online.nprot.2011.372.pdf|pdf]]<br />
<br />
*25. '''Insuk Lee''', Probabilistic functional gene societies. '''''Progress in Biophysics and Molecular Biology''''' 106:435-442 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21281658 pubmed] [[media:Publications_023_n.pdf|pdf]]<br />
<br />
*24. '''Insuk Lee*''', U. Martin Blom, Peggy I. Wang, Jung Eun Shim, and Edward M. Marcotte*. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. '''''Genome Research''''' 21:1109-1121 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21536720 pubmed] [[media:Publications_025_n.pdf|pdf]]<br />
<br />
*23. Young-Su Seo, Mawsheng Chern, Laura E. Bartley, Muho Han, Ki-Hong Jung, '''Insuk Lee''', Harkamal Walia, Todd Richter, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E. Canlas, Randy Ruan, Chang-Jin Park, Xuewel Chen, Sohyun Hwang, Jong-Seong Jeon, and Pamela C. Ronald. Towards establishment of a rice stress response interactome. '''''PLoS Genetics''''' 7(4):e1002020 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21533176 pubmed] [[media:Publications_024.pdf|pdf]]<br />
<br />
==2010==<br />
*22. Ni Huang, '''Insuk Lee''', Edward M.Marcotte, Matthew E.Hurles, Characterising and predicting haploinsufficiency in the human genome, '''''PLoS Genet.''''' 6(10):e1001154(2010) [http://www.ncbi.nlm.nih.gov/pubmed/20976243 pubmed] [[media:Publications_022.pdf|pdf]]<br />
<br />
*21. Eiru Kim, Jaeyoon Shin and '''Insuk Lee''', Assessment of effectiveness of the network-guided genetic screen, '''''Mol Biosyst.''''' 6:1803-1806(2010) [http://www.ncbi.nlm.nih.gov/pubmed/20697632 pubmed] [[media:Publications_021.pdf|pdf]]<br />
<br />
*20. '''Insuk Lee*''', Ben Lehner, Tanya Vavouri, Junha Shin, Andrew G. Fraser, and Edward M. Marcotte, Predicting genetic modifier loci using functional gene networks, '''''Genome Research''''', 20:1143-1153(2010) . co-corresponding author [http://www.ncbi.nlm.nih.gov/pubmed/20538624 pubmed] [[media:Publications_020.pdf|pdf]]<br />
<br />
*19. '''Insuk Lee*''', Bindu Ambaru, Pranjali Thakkar, Edward M Marcotte*, Seung Y Rhee*, Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana, '''''Nature Biotechnology''''', 28:149-156 (2010). ''co-corresponding author'' [http://www.ncbi.nlm.nih.gov/pubmed/20118918 pubmed] [[media:Publications_019.pdf|pdf]]<br />
==2009==<br />
*18. '''Insuk Lee''' and Edward Marcotte. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. p463-475 (2009) [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]<br />
<br />
*17. Zhihua Li, '''Insuk Lee''', Emily Moradi, Nai-Jung Hung, Arlen W. Johnson, Edward M. Marcotte, Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 7(10):e1000213 (2009) [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]<br />
<br />
*16. Ryan S. Gray, Philip B. Abitua, Bogdan J. Wlodarczyk, Heather L. Szabo-Rogers, Otis Blanchard, '''Insuk Lee''', Greg S. Weiss, Karen J. Liu, Edward M. Marcotte, John B. Wallingford, Richard H. Finnell. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 11:1225-32 (2009) '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]<br />
==2008==<br />
*15. Ben Lehner* and '''Insuk Lee*'''. Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 7:217-227 (2008). '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]<br />
<br />
*14. '''Insuk Lee''' and Edward Marcotte. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. p267-278 (2008) [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]<br />
<br />
*13. '''Insuk Lee''', Ben Lehner, Catriona Crombie, Wendy Wong, Andrew G. Fraser, Edward M. Marcotte. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 40:181-188 (2008). '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]]<br />This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)<br />
<br />
==Before 2007==<br />
*12. '''Insuk Lee''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]<br />
<br />
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]<br />
<br />
*10. '''Insuk Lee''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]<br />
<br />
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]<br />
<br />
*8. Insuk Lee, Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]<br />
<br />
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]<br />
<br />
*6. '''Insuk Lee''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)<br />
<br />
*5. '''Insuk Lee''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)<br />
<br />
*4. '''Insuk Lee''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)<br />
<br />
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)<br />
<br />
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998) <br />
<br />
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)<br />
==Patent==<br />
*[https://www.google.com/patents/WO2013055867A1?cl=en&dq=ininventor:%22Insuk+LEE%22&hl=en&sa=X&ei=owFiU5XqMM-B8gXP3YFw&ved=0CDcQ6AEwAA Genes involved in stress response in plants]</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Publications&diff=3240
Publications
2014-07-13T03:19:44Z
<p>Hhj6212: /* 2014 */</p>
<hr />
<div>*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report] <br />
{{#widget:AddHtml<br />
|content=<span id='badgeCont967476' style='width:126px'><a title="Insuk Lee's Profile" href='http://www.researcherid.com/rid/F-7722-2010' target='_blank'><img src='http://labs.researcherid.com/mashlets/badge/rid-idsymbol4.gif' border='0'></a></span><br />
}}<br />
<br />
* '*' co-corresponding authorship<br />
==2014==<br />
*37. Hwang S, Kim E, Yang S, Marcotte EM, '''Lee I''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 May 26 [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]<br />
*36. '''Lee I''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''' 2014 May 23 [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]<br />
*35. Ara Cho, Junha Shin, Sohyun Hwang, Chanyung Kim, Hongsuk Shim, Hyojin Kim, Hanhae Kim, '''Insuk Lee''', WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 May 9 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]<br />
*34. Junha Shin, Tak Lee, Hanhae Kim and '''Insuk Lee''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 10 (1), 24 - 29., (2014) [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]<br />
*33. Hanhae Kim, Junha Shin, Eiru Kim, Hyojin Kim, Sohyun Hwang, Jung Eun Shim, '''Insuk Lee''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 42 (D1): D731-D736., (2014) [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]<br />
<br />
==2013==<br />
*32. Eiru Kim, Hanhae Kim and '''Insuk Lee''', JiffyNet: a web-based instant protein network modeler for newly sequenced species. '''''Nucleic Acids Research''''' 41 (W1): W192-W197., (2013) [http://www.ncbi.nlm.nih.gov/pubmed/23685435 Pubmed][http://nar.oxfordjournals.org/content/early/2013/05/17/nar.gkt419.full.pdf+html pdf]<br />
*31. '''Insuk Lee''', Network approaches to the genetic dissection of phenotypes in animals and humans. '''''Animal Cells and Systems''''' Vol.17,No.2,75-79(2013)[http://www.tandfonline.com/doi/abs/10.1080/19768354.2013.789076 Link]<br />
<br />
==2012==<br />
*30. Peggy I Wang, Sohyun Hwang, Rodney P Kincaid, Christopher S Sullivan, '''Insuk Lee*''', and Edward M Marcotte*. RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. '''''Genome Biology''''' 13:R125 (2012)[http://www.ncbi.nlm.nih.gov/pubmed/23268829 pubmed] <br />
*29. Lee Chae*, '''Insuk Lee*''', Junha Shin, and Seung Yon Rhee*. Towards understanding how molecular networks evolve in plant. '''''Current Opinion in Plant Biology''''' 15:177-184 (2012)[http://www.ncbi.nlm.nih.gov/pubmed/22280840 pubmed] [[media:CurrOpinPlantBiol 15-177.pdf|pdf]]<br />
*28. Stephanie M. Quanbeck, Libuse Brachova, Alexis A. Campbell, Xin Guan, Ann Perera, Kun He, Seung Y. Rhee, Preeti Bais, Julie A. Dickerson, Philip Dixon, Gert Wohlgemuth, Oliver Fiehn, Lenore Barken, Iris Lange, B. Markus Lange, '''Insuk Lee''', Diego Cortes, Carolina Salazar, Joel Shuman, Vladimir Shulaev, David V. Huhman, Lloyd W. Sumner, Mary R. Roth, Ruth Welti, Hilal Ilarslan, Eve S. Wurtele, and Basil J. Nikolau. Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of “unknown function”. '''''Frontiers in Plant Science''''' 3:1-12 (2012) [http://www.ncbi.nlm.nih.gov/pubmed/22645570/ pubmed][[media:Fpls-03-00015.pdf|pdf]]<br />
<br />
==2011==<br />
*27. '''Insuk Lee*''', Young-Su Seo, Dusica Coltrane, Sohyun Hwang, Taeyun Oh, Edward M. Marcotte*, and Pamela C. Ronald*. Genetic dissection of the biotic stress response using a genome-scale gene network for rice. '''''PNAS''''' 108(45):18548-53 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/22042862 pubmed] [[media:PNAS-2011-Lee-18548-53.pdf|pdf]]<br />
<br />
*26. Sohyun Hwang, Seung Y. Rhee*, Edward M. Marcotte*, and '''Insuk Lee*'''. Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana. '''''Nature Protocols''''' 6:1429-1442 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21886106 pubmed][[media:2011.08.25.online.nprot.2011.372.pdf|pdf]]<br />
<br />
*25. '''Insuk Lee''', Probabilistic functional gene societies. '''''Progress in Biophysics and Molecular Biology''''' 106:435-442 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21281658 pubmed] [[media:Publications_023_n.pdf|pdf]]<br />
<br />
*24. '''Insuk Lee*''', U. Martin Blom, Peggy I. Wang, Jung Eun Shim, and Edward M. Marcotte*. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. '''''Genome Research''''' 21:1109-1121 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21536720 pubmed] [[media:Publications_025_n.pdf|pdf]]<br />
<br />
*23. Young-Su Seo, Mawsheng Chern, Laura E. Bartley, Muho Han, Ki-Hong Jung, '''Insuk Lee''', Harkamal Walia, Todd Richter, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E. Canlas, Randy Ruan, Chang-Jin Park, Xuewel Chen, Sohyun Hwang, Jong-Seong Jeon, and Pamela C. Ronald. Towards establishment of a rice stress response interactome. '''''PLoS Genetics''''' 7(4):e1002020 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21533176 pubmed] [[media:Publications_024.pdf|pdf]]<br />
<br />
==2010==<br />
*22. Ni Huang, '''Insuk Lee''', Edward M.Marcotte, Matthew E.Hurles, Characterising and predicting haploinsufficiency in the human genome, '''''PLoS Genet.''''' 6(10):e1001154(2010) [http://www.ncbi.nlm.nih.gov/pubmed/20976243 pubmed] [[media:Publications_022.pdf|pdf]]<br />
<br />
*21. Eiru Kim, Jaeyoon Shin and '''Insuk Lee''', Assessment of effectiveness of the network-guided genetic screen, '''''Mol Biosyst.''''' 6:1803-1806(2010) [http://www.ncbi.nlm.nih.gov/pubmed/20697632 pubmed] [[media:Publications_021.pdf|pdf]]<br />
<br />
*20. '''Insuk Lee*''', Ben Lehner, Tanya Vavouri, Junha Shin, Andrew G. Fraser, and Edward M. Marcotte, Predicting genetic modifier loci using functional gene networks, '''''Genome Research''''', 20:1143-1153(2010) . co-corresponding author [http://www.ncbi.nlm.nih.gov/pubmed/20538624 pubmed] [[media:Publications_020.pdf|pdf]]<br />
<br />
*19. '''Insuk Lee*''', Bindu Ambaru, Pranjali Thakkar, Edward M Marcotte*, Seung Y Rhee*, Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana, '''''Nature Biotechnology''''', 28:149-156 (2010). ''co-corresponding author'' [http://www.ncbi.nlm.nih.gov/pubmed/20118918 pubmed] [[media:Publications_019.pdf|pdf]]<br />
==2009==<br />
*18. '''Insuk Lee''' and Edward Marcotte. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. p463-475 (2009) [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]<br />
<br />
*17. Zhihua Li, '''Insuk Lee''', Emily Moradi, Nai-Jung Hung, Arlen W. Johnson, Edward M. Marcotte, Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 7(10):e1000213 (2009) [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]<br />
<br />
*16. Ryan S. Gray, Philip B. Abitua, Bogdan J. Wlodarczyk, Heather L. Szabo-Rogers, Otis Blanchard, '''Insuk Lee''', Greg S. Weiss, Karen J. Liu, Edward M. Marcotte, John B. Wallingford, Richard H. Finnell. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 11:1225-32 (2009) '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]<br />
==2008==<br />
*15. Ben Lehner* and '''Insuk Lee*'''. Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 7:217-227 (2008). '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]<br />
<br />
*14. '''Insuk Lee''' and Edward Marcotte. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. p267-278 (2008) [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]<br />
<br />
*13. '''Insuk Lee''', Ben Lehner, Catriona Crombie, Wendy Wong, Andrew G. Fraser, Edward M. Marcotte. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 40:181-188 (2008). '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]]<br />This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)<br />
<br />
==Before 2007==<br />
*12. '''Insuk Lee''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]<br />
<br />
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]<br />
<br />
*10. '''Insuk Lee''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]<br />
<br />
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]<br />
<br />
*8. Insuk Lee, Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]<br />
<br />
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]<br />
<br />
*6. '''Insuk Lee''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)<br />
<br />
*5. '''Insuk Lee''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)<br />
<br />
*4. '''Insuk Lee''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)<br />
<br />
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)<br />
<br />
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998) <br />
<br />
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)<br />
==Patent==<br />
*[https://www.google.com/patents/WO2013055867A1?cl=en&dq=ininventor:%22Insuk+LEE%22&hl=en&sa=X&ei=owFiU5XqMM-B8gXP3YFw&ved=0CDcQ6AEwAA Genes involved in stress response in plants]</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=People:HJ_Han&diff=3239
People:HJ Han
2014-07-03T03:11:59Z
<p>Hhj6212: </p>
<hr />
<div>{|<br />
|[[File:heonjong.jpg|300px]]<br />
=== Heonjong Han ===<br />
*'''B.Eng''', Yonsei University, School of Engineering, Department of Biotechnology (02/2013).<br />
<pre><br />
*E-mail : hhj6212(at)gmail.com</pre><br />
|}</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=People:HJ_Han&diff=3238
People:HJ Han
2014-07-03T03:10:40Z
<p>Hhj6212: </p>
<hr />
<div>=== Heonjong Han ===<br />
*'''B.Eng''', Yonsei University, School of Engineering, Department of Biotechnology (02/2013).<br />
<pre><br />
*E-mail : hhj6212(at)gmail.com</pre></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=People:DS_Bae&diff=3237
People:DS Bae
2014-07-03T03:08:05Z
<p>Hhj6212: /* Da Som Bae */</p>
<hr />
<div>===Da Som Bae===<br />
{|<br />
|[[File:배다솜.jpg|300px]]<br />
|(2014- )'''Ph.D program student''', Yonsei University, Department of Biotechnology.<br />
(2008-2013) Department of Bioinformatics, Soongsil University <br />
<br />
|}</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=People:DS_Bae&diff=3236
People:DS Bae
2014-07-03T03:07:51Z
<p>Hhj6212: /* Da Som Bae */</p>
<hr />
<div>===Da Som Bae===<br />
{|<br />
|[[File:배다솜.jpg|300px]]<br />
|(2014-)*'''Ph.D program student''', Yonsei University, Department of Biotechnology.<br />
(2008-2013) Department of Bioinformatics, Soongsil University <br />
<br />
|}</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=People:DS_Bae&diff=3235
People:DS Bae
2014-07-03T03:07:28Z
<p>Hhj6212: /* Da Som Bae */</p>
<hr />
<div>===Da Som Bae===<br />
{|<br />
|[[File:배다솜.jpg|300px]]<br />
|*'''Ph.D program student''', Yonsei University, Department of Biotechnology (09/2014 - ).<br />
(2008-2013) Department of Bioinformatics, Soongsil University <br />
<br />
|}</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=File:%EB%B0%B0%EB%8B%A4%EC%86%9C.jpg&diff=3234
File:배다솜.jpg
2014-07-03T03:04:49Z
<p>Hhj6212: Hhj6212 uploaded a new version of &quot;File:배다솜.jpg&quot;</p>
<hr />
<div></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=File:Heonjong.jpg&diff=3233
File:Heonjong.jpg
2014-07-03T02:51:43Z
<p>Hhj6212: Hhj6212 uploaded a new version of &quot;File:Heonjong.jpg&quot;</p>
<hr />
<div></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=File:2014_hjhan.JPG&diff=3232
File:2014 hjhan.JPG
2014-07-03T02:49:20Z
<p>Hhj6212: </p>
<hr />
<div></div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=People&diff=3228
People
2014-07-02T05:10:40Z
<p>Hhj6212: /* Research Staffs */</p>
<hr />
<div>__NOTOC__<br />
=='''Principal Investigator'''==<br />
{|border="0" width="150"<br />
|align="center"|[[File:People_ISLee_03.jpg|77px|link=people:IS_Lee]]<br />
|<br />
|<br />
|-<br />
|align="center"|[[people:IS_Lee|Insuk Lee]]<br />
|<br />
|<br />
|-<br />
|}<br />
<br />
=='''Research Fellows'''==<br />
{|border="0" width="450"<br />
|align="center"|[[File:People_JE_Shim_EDIT.JPG|70px|link=people:JE_Shim]]<br />
|align="center" cell-width="200"|[[File:People_SYHwang.JPG|70px|link=people:SH_Hwang]]<br />
|align="center"|[[File:People_Junha_Shin_cut.gif|70px|link=people:JH_Shin]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Jung Eun Shim]]<br />
|align="center"|[[people:SH_Hwang|SoHyun Hwang]]<br />
|align="center"|[[people:JH_Shin|JunHa Shin]]<br />
|-<br />
|align="center"|[[people:JE_Shim|Research Professor]]<br />
|align="center"|[[people:SH_Hwang|Research Professor]]<br />
|align="center"|[[people:JH_Shin|Postdoc Fellow]]<br />
|}<br />
<br />
=='''Graduate Students'''==<br />
{|border="0" width="600"<br />
|align="center"|[[File:People_HHKim_cut.jpg|70px|link=people:HH_Kim]]<br />
|align="center"|[[File:People_ARCho_cut.png|70px|link=people:AR_Cho]]<br />
|align="center" cell-width="200"|[[File:Banmyungham.JPG|70px|link=people:ER_Kim]]<br />
|align="center"|[[File:Tak_sajin3.jpg|70px|link=people:T_Lee]]<br />
|-<br />
|align="center"|[[people:HH_Kim|HanHae Kim]]<br />
|align="center"|[[people:AR_Cho|ARa Cho]]<br />
|align="center"|[[people:ER_Kim|Eiru Kim]]<br />
|align="center"|[[people:T_Lee|Tak Lee]]<br />
|-<br />
|align="center"|[[people:HH_Kim|PhD course]]<br />
|align="center"|[[people:AR_Cho|PhD course]]<br />
|align="center"|[[people:ER_Kim|PhD course]]<br />
|align="center"|[[people:T_Lee|PhD course]]<br />
|-<br />
|align="center"|[[File:People_KSKim.jpg|70px|link=people:KS_Kim]]<br />
|align="center"|[[File:heonjong.jpg|70px|link=people:HJ_Han]]<br />
|align="center"|[[File:Hjkim.jpg|70px|link=People:HJ_Kim]]<br />
|align="center"|[[File:HSshim.jpg|70px|link=people:HS_Shim]]<br />
|-<br />
|align="center"|[[people:KS_Kim|Kyung Soo Kim]]<br />
|align="center"|[[people:HJ_Han|Heon Jong Han]]<br />
|align="center"|[[People:HJ Kim|HyoJin Kim]]<br />
|align="center"|[[people:HS_Shim|HongSeok Shim]]<br />
|-<br />
|align="center"|[[people:HJ_Han|PhD course]]<br />
|align="center"|[[People:HJ Kim|PhD course]]<br />
|align="center"|[[people:HS_Shim|MS course]]<br />
|align="center"|[[people:KS_Kim|MS course]]<br />
|}<br />
<br />
=='''Research Staffs'''==<br />
{|border="0" width="450"<br />
|align="center"|[[File:Smyang.jpg|70px|link=people:SM_Yang]]<br />
|align="center"|[[File:SYLee.jpg|80px|link=people:SY_Lee]]<br />
|align="center"|[[File:AYYoon.jpg|80px|link=people:AY_Yoon]]<br />
|-<br />
|align="center"|[[people:SM_Yang|SunMo Yang]]<br />
|align="center"|[[people:SY_Lee|Sangyoung Lee]]<br />
|align="center"|[[people:AY_Yoon|Ayeong Yoon]]<br />
|-<br />
|align="center"|[[people:SM_Yang|System Administrator]]<br />
|align="center"|[[people:SY_Lee|Research Assistant]]<br />
|align="center"|[[people:AY_Yoon|Research Assistant]]<br />
|}<br />
<br />
=='''Undergraduate Students'''==<br />
{|border="0" width="450"<br />
|align="center"|[[File:배다솜.jpg|70px|link=People:DS Bae]]<br />
|align="center"|[[File:CY KIM.jpg|70px|link=People:CY_Kim]]<br />
|align="center"|[[File:BHKang.jpg|70px|link=People:BH_Kang]]<br />
|-<br />
|align="center"|[[People:DS Bae|Dasom Bae]]<br />
|align="center"|[[People:CY Kim|ChanYoung Kim]]<br />
|align="center"|[[People:BH_Kang|ByungHee Kang]]<br />
|}<br />
<br />
=='''Visiting scientists'''==<br />
<br />
=='''Alumni'''==<br />
*Former Post-docs and Staff Scientists<br />
**Taeyun Oh (2009.5-2011.12), current position; US-DOE Postdoc fellow, University of California at Davis (Pam Ronald's Lab)<br />
**Samuel Beck (2011.2-2011.12), current position; Postdoc fellow, University of Texas at Austin (Jonghwan Kim's Lab)<br />
**Jawon Song (2011.1-2012.5), current position; Research Scientist, Texas Advanced Computing Center, Austin, TX, USA<br />
**Yoonhee Ko (2012.8-2014.2), current position; Fellow, Severance Medical center (Yonsei Medical school)<br />
**Jonghoon Lee (2013.10-2014.2), current position; Assistant Professor, CHA Medical school <br />
<br />
*Former Graduate Students<br />
**Sungou Ji (2009.9-2011.8), MS, went to a graduate school, Sanger Genome Institute, Cambridge University, UK (Research field: Statistical Genomics)<br />
<br />
*Former Visiting Scientists<br />
**Minkyung Shin (2012.3-2012.7), went to a graduate school, University of Southern California, USA<br />
<br />
*Former Undergraduate Students<br />
**Ila Shin, went to a medical school (Yonsei Univ.)<br />
**Yoonkyung Ko<br />
**Sangyo Park, went to a law school (Kyounghee Univ.)<br />
**Jayoon Shin, went to a medical school (Pusan National Univ.)<br />
**Dongjoo Sun, went to a dental school (Wongwang Univ.)<br />
**Eulsoo Kim<br />
**Myungwhan Lee, went to a medical school (Yonsei Univ.)<br />
**Moonhee Lee<br />
**Jinhyun Ju, went to a graduate school, Cornell Medical School, NY, USA (Research field: Computational Systems Biology)<br />
**Haeyoung Shin, went to a graduate school, Brown University, USA (Research field: Computational Neuroscience)<br />
**Joonghee Soh, went to a graduate school, KAIST, Korea (Research field: Culture Technology)<br />
**Hee Jung Cho<br />
**TaeHwan Kim<br />
**Joohyung Kim</div>
Hhj6212
https://netbiolab.org/wiki/index.php?title=Welcome_to_Network_Biology_Laboratory&diff=3224
Welcome to Network Biology Laboratory
2014-07-02T02:17:32Z
<p>Hhj6212: /* Oral Presentation */</p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0"<br />
|rowspan="2"|<br />
[[File :2014group3.JPG|544px|center|middle|Main Photo]]<br />
<br />
|colspan=2|<br />
[http://www2.clustrmaps.com/user/563d3fa7 http://www2.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]<br />
|-<br />
|width="185" style="text-align:center;vertical-align:top;padding:0 0 0 5px;"|<br />
=== Oral Presentation ===<br />
<pre style="text-align:left;"><br />
HH Kim <br />
JE Shim <br />
T Lee **<br />
AR Cho <br />
HJ Han<br />
HS Shim <br />
JH Shin <br />
KS Kim<br />
ER Kim<br />
HJ Kim <br />
CY Kim<br />
DS Bae <br />
BH Kang <br />
</pre><br />
<br />
|-<br />
<br />
|colspan=3|<br />
<br />
===Contact Informations===<br />
<pre><br />
Yonsei University 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea <br />
Office: Engineering Research Park B118DA<br />
<br />
+82-70-8625-5205 <br />
</pre><br />
|}</div>
Hhj6212