===Chan Young Kim===
{|
|[[File:20161001_131856.jpg|500px]]
|'''Ph.D program student''', Department of Biotechnology, Yonsei University (2015~)
B.E. Department of Biotechnology, Yonsei University. (Feb 2015)

B.E. Department of Computer Science, Yonsei University. (Feb 2015)

<pre>*E-mail : vxterran(at)gmail.com</pre>

Research Interest
* Functional metagenomics
* Network Biology
|}

==Publications==
* '''Kim CY*''', Lee M, Lee K, Yoon SS, Lee I**, Network-based genetic investigation of virulence-associated phenotypes in methicillin-resistant Staphylococcus aureus, Scientific Reports 2018 July 17; 8:10796
* '''Kim CY*''', Lee I**, Functional gene networks based on the gene neighborhood in metagenomes, Animal Cells and Systems 2017 Sept 29; 21:301-306
* Shim H*, Kim JH*, '''Kim CY*''', Hwang S, Kim H, Yang S, Lee JE**, Lee I**, Function-driven discovery of disease genes in zebraﬁsh using an integrated genomics big data resource,Nucleic Acids Research 2016 Nov 16;44(20):9611-9623
* Hwang S*, '''Kim CY*''', Ji SG, Go J, Kim H, Yang S, Kim HJ, Cho A, Yoon SS**, Lee I**. Network-assisted investigation of virulence and antibiotic-resistance systems in Pseudomonas aeruginosa.Scientific Reports 2016 May 19; 6:26223.

People

2018-08-22T10:48:37Z

Cykim: /* Graduate Students */

__NOTOC__
=='''Principal Investigator'''==
{|border="0" width="150"
|align="center"|[[File:이인석-2011사진.jpg|77px|link=people:IS_Lee]]
|-
|align="center"|[[people:IS_Lee|Insuk Lee]]
|-
|}

=='''Research Professor/Postdoc Fellow/Research Staff'''==
{|border="0" width="300"
|align="center"|[[File:Smyang.jpg|70px|link=people:SM_Yang]]
|align="center"|[[File:SYLee.jpg|70px|link=people:SY_Lee]]
|-
|align="center"|[[people:SM_Yang|Sunmo Yang]]
|align="center"|[[people:SY_Lee|Sangyoung Lee]]
|-
|align="center"|[[people:SM_Yang|Bioinformatics Programmer System Administrator]]
|align="center"|[[people:SY_Lee|Senior Research Assistant]]
|}

=='''Graduate Students'''==
{|border="0" width="800"

|align="center" |[[File:heonjong.jpg|70px|link=people:HJ_Han]]
|align="center" |[[File:People_KSKim.jpg|70px|link=people:KS_Kim]]
|align="center"|[[File:배다솜.jpg|70px|link=People:DS Bae]]
|align="center"|[[File:cykim.PNG|70px|link=People:CY_Kim]]
|align="center"|[[File:Cho_JW.png|70px|link=People:J_Cho]]
|align="center"|[[File:SHLee_outside.jpg|70px|link=People:S_Lee]]
|-

|align="center"|[[people:HJ_Han|Heonjong Han]]
|align="center"|[[people:KS_Kim|Kyungsoo Kim]]
|align="center"|[[People:DS Bae|Dasom Bae]]
|align="center"|[[People:CY Kim|Chan Yeong Kim]]
|align="center"|[[People:J_Cho|Jae Won Cho]]
|align="center"|[[People:S_Lee|Sungho Lee]]
|-

|align="center"|[[People:HJ_Han|PhD candidate (2013.3 - )]]
|align="center"|[[people:KS_Kim|PhD candidate (2013.3 - )]]
|align="center"|[[people:DS Bae|PhD course (2014.9 - )]]
|align="center"|[[people:CY Kim|PhD candidate (2015.3 - )]]
|align="center"|[[people:J_Cho|PhD candidate (2016.9 - )]]
|align="center"|[[People:S_Lee|PhD course (2017.3 - )]]
|}

=='''Undergraduate Students'''==
**Junha Cha
**Sung Jun Lim
**Hojeong Keum
**Soyun Kong

=='''Visiting scientists/students'''==

=='''Alumni'''==
*Former Post-docs and Staff Scientists
**Taeyun Oh (2009.5-2011.12), currently Deputy Principal Consultant (인실리코젠 생명정보분석컨설턴트), [http://www.insilicogen.com INSILICOGEN], Korea
**Sohyun Hwang (2010.3-2015.8), currently Assistant Professor (차의과대학 의과학과 교수), [http://bt.cha.ac.kr/ Department of Biomedical Science, CHA University], Korea
**Samuel Beck (2011.2-2011.12), currently Assistant Professor of Computational Biology, The Mount Desert Island Biological Laboratory, Maine, USA (미국 MDI 생명과학연구소 교수), [https://mdibl.org/faculty/sam-beck-ph-d/ Lab Homepage]
**Jawon Song (2011.1-2012.5), currently Research Associate (미국 텍사스슈퍼컴퓨팅센터 선임연구원), [https://www.tacc.utexas.edu/about/directory/jawon-song Texas Advanced Computing Center], Austin, TX, USA
**Yoonhee Ko (2012.8-2014.2), currently Assistant Professor (한국외국어대 바이오공학과 교수), [http://bme.hufs.ac.kr/ Department of Biomedical Engineering, Hankuk University of Foreign Studies], Korea
**Jonghoon Lee (2013.10-2014.2), currently Assistant Professor (차의과대학 식품생명공학과 교수), [http://fsb.cha.ac.kr/ Department of Food Science and Biotechnology, CHA University], Korea
**Jung Eun Shim (2009.8-2017.11), currently Researcher at Yonsei Genomics Center Bioinformatics Data Analysis Core (연세의료원 유전체센터 생명정보분석코어 선임연구원)

*Former Graduate Students (PhD)
**Junha Shin (2008.9-2014.2), PhD; currently Postdoc Fellow, University of Wisconsin-Madison (미국 위스콘신대 박사후연구원), USA [https://roylab.discovery.wisc.edu/ Roy Lab]
**Hanhae Kim (2008.9-2015.2), PhD; currently Associate Research Fellow (한국과학기술기획평가원 부연구위원), [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)]
**Ara Cho (2008.9-2015.2), PhD; currently Associate Research Fellow (한국과학기술기획평가원 부연구위원), [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)]
**Eiru Kim (2010.9-2016.8), PhD; currently Postdoc Fellow, MD Anderson Cancer Center, Texas, USA (미국 엠디앤더슨암센터 박사후연구원) [http://www.hart-lab.org/ Hart Lab]
**Tak Lee (2011.3-2017.2), PhD; currently Postdoc Fellow, Sainsbury Laboratory at University of Cambridge, UK (영국 캠브리지대학 박사후연구원) [https://www.slcu.cam.ac.uk/research/oldroyd-group Oldroyd Lab] [https://www.slcu.cam.ac.uk/research/ahnert-group Ahnert Lab]
*Former Graduate Students (Master)
**Sun-Gou Ji (2009.9-2011.8), M.Eng.; PhD from University of Cambridge (Sanger Genome center); currently R&D engineer at [https://www.sbgenomics.com/ Seven Bridges], USA
**Hyojin Kim (2013.3-2015.2), M.Eng.; currently Bioinformatics Scientist, Aachen University, Germany
**Hongseok Shim (2013.9-2015.8), M.Eng.;
**Sunmo Yang (2014.9-2017.2), M.Eng. currently Bioinformatics programmer, Yonsei University
**Muyoung Lee (2016.3-2018.2), M.Eng.

*Former Visiting Scientists/Students
**Minkyung Shin (2012.3-2012.7), went to graduate school (University of Southern California)
**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
**Susie Shin (2013 summer high school student intern), went to Vanderbilt University, USA
**Hyunjin Cho (Johns Hopkins University, Bioinformatics), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA
**Michael Chung (2016.8-2016.12)

*Former Undergraduate Students
**Ila Shin, went to medical school (Yonsei Univ.)
**Yoonkyung Ko
**Sangyo Park, went to law school (Kyounghee Univ.)
**Jayoon Shin, went to medical school (Pusan National Univ.)
**Dongjoo Sun, went to dental school (Wongwang Univ.)
**Eulsoo Kim
**Myungwhan Lee, went to medical school (Yonsei Univ.)
**Moonhee Lee, went to graduate school (University of Amsterdam, Netherlands)
**Jinhyun Ju, went to graduate school (Cornell Medical School, Computational Systems Biology); Currently Bioinformatics Scientist, Illumina, San Diego, USA (현재 미국 Illumina 본사 근무)
**Haeyoung Shin, went to graduate school (Brown University, Computational Neuroscience)
**Joonghee Soh, went to graduate school (KAIST, Culture Technology)
**Hee Jung Cho, went to graduate school (UC Berkeley)
**TaeHwan Kim, went to medical school
**Joohyung Kim, went to medical school (Kyungpook National Univ.)
**Donghyun Shin, went to medical school (Yonsei Univ.)
**Sunphil Kim
**Jaeho Shim
**Seunghyun Shin
**Aejoo Hong
**Changbae Bang, went to medical school (Yonsei Univ.)
**Seoyoung Choi
**Dabin Jung
**Byunghee Kang, went to graduate school (PosTech)
**Borem Nam
**Seungun Lee
**Yeaji Kim
**Sangyoung Lee
**Heejun Jang, went to KIST as Research Assistant
**Jungha Lee, went to graduate school (Seoul National Univ.)
**Seunghyun Wang, went to graduate school (KAIST)
**Dong-Min Yang
**Doo-Hee Lee
**Ji-Yoon Lee
**Suk-Jae Han
**Ji-Eun Han
**Yuri Ko
**Sung-Woo Kim
**Woosung Kwon

File:Cykim.PNG

2018-08-22T10:48:14Z

Cykim:

Software

2018-08-13T07:02:43Z

Cykim: /* Human and Laboratory Animals */

__NOTOC__
=='''Network Medicine Tools '''==
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST''': A reference database of TF-target interactions in human and mouse

[[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation data

[[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

[[File:Coexpedia.png |150px|link=http://www.coexpedia.org]] '''COEXPEDIA''': Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)

[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN''': Network-assisted prediction of disease pathways in model organisms

[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only)

=='''Co-functional Gene Networks'''==

==''Human and Laboratory Animals''==
{|border="0" width="500"
|align="center"|[[file:HumanNet_logo_with_title.png|150px|link=http://www.inetbio.org/humannet]]
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
|align="center"|[[file:danionet_logo.png|150px|link=http://www.inetbio.org/danionet]]
|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]
|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
|-
|align="center"|''Homo sapiens''
|align="center"|''Mus musculus''
|align="center"|''Danio rerio''
|align="center"|''Drosophila melanogaster''
|align="center"|''Caenorhabditis elegans''
|}

==''Plants''==
{|border="0" width="400"
|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]]
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=http://www.inetbio.org/maizenet]]
|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
|align="center"|[[File:WheatNet_logo.png|150px|link=http://www.inetbio.org/wheatnet]]
|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]
|align="center"|[[File:Tomatonet_logo.png|150px|link=http://www.inetbio.org/tomatonet]]
|-
|align="center"|''Arabidopsis thaliana''
|align="center"|''Zea mays''
|align="center"|''Oryza sativa''
|align="center"|''Triticum aestivum''
|align="center"|''Glycine max''
|align="center"|''Solanum lycopersicum''
|}

==''Fungi''==
{|border="0" width="200"
|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]]
|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]]
|-
|align="center"|''Saccharomyces cerevisiae''
|align="center"|''Cryptococcus neoformans''
|}

==''Bacteria''==
{|border="0" width="200"
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]]
|align="center"|[[File:Staphnet_logo.JPG|150px|link=http://www.inetbio.org/staphnet]]
|align="center"|[[File:KlebNet_logo.png|150px|link=http://www.inetbio.org/klebnet]]
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
|align="center"|[[File:XooNet_logo.png|150px|link=http://www.inetbio.org/xoonet]]
|-
|align="center"|''Pseudomonas aeruginosa (human pathogen)''
|align="center"|Methicillin-resistant ''Staphylococcus aureus (human pathogen)''
|align="center"|''Klebsiella pneumoniae (human pathogen)''
|align="center"|''Escherichia coli (popular lab/factory bacterial species)''
|align="center"|''Xanthomonas oryzae pv. oryzae (rice pathogen)''
|}

==''Build your own co-functional networks''==
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]]
'''JiffyNet''': Instant gene network building server for newly sequenced species

=='''Network-augmented GWAS Analysis for Arabidopsis'''==
[[File:araGWAB_logo.png|150px|link=http://www.inetbio.org/aragwab]]
'''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana''

=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
[[WMI|<big>'''Project Page'''</big>]]

=='''Domain2Pathway by Pathway Specificity (PS) '''==
[[PS|<big>'''Project Page'''</big>]]

Software

2018-08-13T07:02:13Z

Cykim: /* Human and Laboratory Animals */

__NOTOC__
=='''Network Medicine Tools '''==
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST''': A reference database of TF-target interactions in human and mouse

[[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation data

[[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

[[File:Coexpedia.png |150px|link=http://www.coexpedia.org]] '''COEXPEDIA''': Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)

[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN''': Network-assisted prediction of disease pathways in model organisms

[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only)

=='''Co-functional Gene Networks'''==

==''Human and Laboratory Animals''==
{|border="0" width="500"
|align="center"|[[file:HumanNet_logo_with_title.png|150px|link=http://wwww.inetbio.org/humannet]]
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
|align="center"|[[file:danionet_logo.png|150px|link=http://www.inetbio.org/danionet]]
|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]
|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
|-
|align="center"|''Homo sapiens''
|align="center"|''Mus musculus''
|align="center"|''Danio rerio''
|align="center"|''Drosophila melanogaster''
|align="center"|''Caenorhabditis elegans''
|}

==''Plants''==
{|border="0" width="400"
|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]]
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=http://www.inetbio.org/maizenet]]
|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
|align="center"|[[File:WheatNet_logo.png|150px|link=http://www.inetbio.org/wheatnet]]
|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]
|align="center"|[[File:Tomatonet_logo.png|150px|link=http://www.inetbio.org/tomatonet]]
|-
|align="center"|''Arabidopsis thaliana''
|align="center"|''Zea mays''
|align="center"|''Oryza sativa''
|align="center"|''Triticum aestivum''
|align="center"|''Glycine max''
|align="center"|''Solanum lycopersicum''
|}

==''Fungi''==
{|border="0" width="200"
|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]]
|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]]
|-
|align="center"|''Saccharomyces cerevisiae''
|align="center"|''Cryptococcus neoformans''
|}

==''Bacteria''==
{|border="0" width="200"
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]]
|align="center"|[[File:Staphnet_logo.JPG|150px|link=http://www.inetbio.org/staphnet]]
|align="center"|[[File:KlebNet_logo.png|150px|link=http://www.inetbio.org/klebnet]]
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
|align="center"|[[File:XooNet_logo.png|150px|link=http://www.inetbio.org/xoonet]]
|-
|align="center"|''Pseudomonas aeruginosa (human pathogen)''
|align="center"|Methicillin-resistant ''Staphylococcus aureus (human pathogen)''
|align="center"|''Klebsiella pneumoniae (human pathogen)''
|align="center"|''Escherichia coli (popular lab/factory bacterial species)''
|align="center"|''Xanthomonas oryzae pv. oryzae (rice pathogen)''
|}

==''Build your own co-functional networks''==
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]]
'''JiffyNet''': Instant gene network building server for newly sequenced species

=='''Network-augmented GWAS Analysis for Arabidopsis'''==
[[File:araGWAB_logo.png|150px|link=http://www.inetbio.org/aragwab]]
'''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana''

=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
[[WMI|<big>'''Project Page'''</big>]]

=='''Domain2Pathway by Pathway Specificity (PS) '''==
[[PS|<big>'''Project Page'''</big>]]

2018-05-14T06:39:03Z

Cykim: /* Data for 2018 netbiolab experiment */

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

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

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

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

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

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

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

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

Welcome to Network Biology Laboratory

2017-11-15T07:50:06Z

Cykim: /* Oral Presentation */

__NOTOC__

{|border = "0" valign="top"
|rowspan="2" style="padding-right:20px;"|
[[File :groupphoto_20161208_crop.jpg|580px|center|middle|Main Photo]]

|colspan=2|
=== Research Keyword Cloud (2012-2016)===
<div>{{#widget:AddHtml|content=<img src="../wiki/cloud2.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div>
|-
|

=== Oral Presentation ===
{|class=wikitable style="text-align:center;"
|-
|style="width:65px"| HJ Han
|style="width:65px"| KS Kim
|style="width:65px"| CY Kim
|-
| DS Bae
| JW Cho
| SH Lee*
|-
|}
|

=== Visitors Trend ===
[https://www.clustrmaps.com/map/Netbiolab.org https://www.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]
|-
|colspan=3|
===Contact Informations===
<pre>
Yonsei University
50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
Science Research Center S323 (Lab) S328 (Professor's Office)
+82-70-8625-5205
</pre>
|}

File:Poster Presentation.jpg

2017-11-06T05:14:45Z

Cykim:

People:Album:2017 11th AYRCOB, GIW

2017-11-06T05:14:20Z

People:CY Kim

2017-10-18T04:58:37Z

Cykim:

===Chan Young Kim===
{|
|[[File:20161001_131856.jpg|500px]]
|'''Ph.D program student'''(2015~) Department of Biotechnology, Yonsei University
(2010-2014) Department of Biotechnology, Yonsei University

<pre>*E-mail : vxterran(at)gmail.com</pre>
|}

==Publications==
* '''Kim CY*''', Lee I**, Functional gene networks based on the gene neighborhood in metagenomes, Animal Cells and Systems 2017 Sept 29; 21:301-306
* Shim H*, Kim JH*, '''Kim CY*''', Hwang S, Kim H, Yang S, Lee JE**, Lee I**, Function-driven discovery of disease genes in zebraﬁsh using an integrated genomics big data resource,Nucleic Acids Research 2016 Nov 16;44(20):9611-9623
* Hwang S*, '''Kim CY*''', Ji SG, Go J, Kim H, Yang S, Kim HJ, Cho A, Yoon SS**, Lee I**. Network-assisted investigation of virulence and antibiotic-resistance systems in Pseudomonas aeruginosa.Scientific Reports 2016 May 19; 6:26223.

Welcome to Network Biology Laboratory

2017-09-13T10:32:09Z

Cykim: /* Oral Presentation */

__NOTOC__

{|border = "0" valign="top"
|rowspan="2" style="padding-right:20px;"|
[[File :groupphoto_20161208_crop.jpg|580px|center|middle|Main Photo]]

|colspan=2|
=== Research Keyword Cloud (2012-2016)===
<div>{{#widget:AddHtml|content=<img src="../wiki/cloud2.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div>
|-
|

=== Oral Presentation ===
{|class=wikitable style="text-align:center;"
|-
|style="width:65px"| JE Shim
|style="width:65px"| T Lee
|style="width:65px"| HJ Han
|-
| KS Kim
| CY Kim*
| DS Bae
|-
| JW Cho
| SH Lee
|
|-
|}
|

=== Visitors Trend ===
[https://www.clustrmaps.com/map/Netbiolab.org https://www.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]
|-
|colspan=3|
===Contact Informations===
<pre>
Yonsei University
50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
Science Research Center S323 (Lab) S328 (Professor's Office)
+82-70-8625-5205
</pre>
|}

Software

2017-08-31T07:47:37Z

Cykim: /* Bacteria */

__NOTOC__
=='''Co-functional gene networks'''==

==''Human and Laboratory Animals''==
{|border="0" width="500"
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
|align="center"|[[file:danionet_logo.png|150px|link=http://www.inetbio.org/danionet]]
|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]
|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
|-
|align="center"|''Homo sapiens''
|align="center"|''Mus musculus''
|align="center"|''Danio rerio''
|align="center"|''Drosophila melanogaster''
|align="center"|''Caenorhabditis elegans''
|}

==''Plants''==
{|border="0" width="400"
|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]]
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=http://www.inetbio.org/maizenet]]
|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
|align="center"|[[File:WheatNet_logo.png|150px|link=http://www.inetbio.org/wheatnet]]
|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]
|align="center"|[[File:Tomatonet_logo.png|150px|link=http://www.inetbio.org/tomatonet]]
|-
|align="center"|''Arabidopsis thaliana''
|align="center"|''Zea mays''
|align="center"|''Oryza sativa''
|align="center"|''Triticum aestivum''
|align="center"|''Glycine max''
|align="center"|''Solanum lycopersicum''
|}

==''Fungi''==
{|border="0" width="200"
|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]]
|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]]
|-
|align="center"|''Saccharomyces cerevisiae''
|align="center"|''Cryptococcus neoformans''
|}

==''Bacteria''==
{|border="0" width="200"
|align="center"|[[File:Staphnet_logo.JPG|150px|link=http://www.inetbio.org/staphnet]]
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]]
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
|align="center"|[[File:XooNet_logo.png|150px|link=http://www.inetbio.org/xoonet]]
|-
|align="center"|Methicillin-resistant ''Staphylococcus aureus''
|align="center"|''Pseudomonas aeruginosa''
|align="center"|''Escherichia coli''
|align="center"|''Xanthomonas oryzae pv. oryzae''
|}

==''Build your own co-functional networks''==
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]]
'''JiffyNet''': Instant gene network building server for newly sequenced species

=='''Transcriptional Regulatory Networks'''==
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST''': A reference database of TF-target interactions in human and mouse

=='''Network-based Disease Research Servers'''==
[[File:Coexpedia.png |150px|link=http://www.coexpedia.org]] '''COEXPEDIA''': Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)

[[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

[[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation data

[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN''': Network-assisted prediction of disease pathways in model organisms

[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only)

=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
[[WMI|<big>'''Project Page'''</big>]]

File:Staphnet logo.JPG

2017-08-31T07:46:59Z

Cykim:

Publications

2017-08-16T01:51:58Z

Cykim: /* 2015 (14) */

* [http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
* [http://www.researcherid.com/rid/F-7722-2010 {{#widget:AddHtml|content=<img src='https://labs.researcherid.com/mashlets/badge/rid-idsymbol4.gif' border='0' />}}]
* '*' First authors; '**' Corresponding authors;
==2017 (9)==
*70. Lee T*, Hwang S*, Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
*69. Lee T*, '''Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
*68. Shim JE*, Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 Apr 26; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
*67. Kim E*, '''Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
*66. Shim JE*, Lee T*, '''Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [http://www.tandfonline.com/doi/full/10.1080/19768354.2017.1284156 article link]
*65. Kim H*, Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
*64. Jang K*, Kim K, Cho A, '''Lee I''', Choi JK**, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]

==2016 (10)==
*61. Shin J**, '''Lee I**''', Construction of Functional Gene Networks Using Phylogenetic Profiles. '''''Methods in Molecular Biology''''' 2016 Nov 29; 1526:87-98 [http://www.ncbi.nlm.nih.gov/pubmed/27896737 pubmed]
*60. Shim H*, Kim JH*, Kim CY*, Hwang S, Kim H, Yang S, Lee JE**, '''Lee I**''', Function-driven discovery of disease genes in zebraﬁsh using an integrated genomics big data resource,'''''Nucleic Acids Research''''' 2016 Nov 16;44(20):9611-9623 [http://www.ncbi.nlm.nih.gov/pubmed/27903883 pubmed]
*59. Shim JE*, '''Lee I**''' Weighted mutual information analysis substantially improves domain-based functional network models. '''''Bioinformatics''''' 2016 Sep 15;32(18):2824-30 [http://www.ncbi.nlm.nih.gov/pubmed/27207946 pubmed]
*58. Lee JY*, Kim E*, Choi SM, Kim DW, Kim KP, '''Lee I**''', Kim HS** Microvesicles from brain-extract—treated mesenchymal stem cells improve neurological functions in a rat model of ischemic stroke. '''''Scientific Reports''''' 2016 Sep 9; 6:33038 [http://www.ncbi.nlm.nih.gov/pubmed/27609711 pubmed]
*57. Kim SM*, Kim JW, Kwak TH, Park SW, Kim KP, Park H, Lim KT, Kang K, Kim J, Yang JH, Han H, '''Lee I''', Hyun JK, Bae YM, Schöler HR, Lee HT, Han DW** Generation of Integration-free Induced Neural Stem Cells from Mouse Fibroblasts. '''''J Biol Chem'''''. 2016 Jul 1. 291(27):14199-212. [http://www.ncbi.nlm.nih.gov/pubmed/27189941 pubmed]
*56. Cho A*, Shim JE, Kim E, Supek F, Lehner B**, '''Lee I**'''. MUFFINN: cancer gene discovery via network analysis of somatic mutation data. '''''Genome Biology''''' 2016 June 23;17(1):129 [http://www.ncbi.nlm.nih.gov/pubmed/27333808 pubmed]
*55. Hwang S*, Kim CY*, Ji SG, Go J, Kim H, Yang S, Kim HJ, Cho A, Yoon SS**, '''Lee I**'''. Network-assisted investigation of virulence and antibiotic-resistance systems in Pseudomonas aeruginosa.'''''Scientific Reports''''' 2016 May 19; 6:26223. [http://www.ncbi.nlm.nih.gov/pubmed/27194047 pubmed]
*54. Yoon MY*, Min KB, Lee KM, Yoon Y, Kim Y, Oh YT, Lee K, Chun J, Kim BY, Yoon SH, '''Lee I''', Kim CY, Yoon SS**,. A single gene of a commensal microbe affects host susceptibility to enteric infection.'''''Nature Communications''''' 2016 May 13; 7:11606. [http://www.ncbi.nlm.nih.gov/pubmed/27173141 pubmed]
*53. Jo J*, Hwang S*, Kim HJ*, Hong S, Lee JE, Lee SG, Baek A, Han H, Lee JI, '''Lee I**''', Lee DR**. An integrated systems biology approach identifies positive cofactor 4 as a factor that increases reprogramming efficiency.'''''Nucleic Acids Research''''' 2016 Feb 18; 44(3):1203-15.[http://www.ncbi.nlm.nih.gov/pubmed/26740582 pubmed]
*52. Kim E*, Hwang S, Kim H, Shim H, Kang B, Yang S, Shim JH, Shin SY, Marcotte EM, '''Lee I**'''. MouseNet v2: A database of gene networks for studying the laboratory mouse and eight other model vertebrates,'''''Nucleic Acids Research''''' 2016 Jan 4;44(D1):D848-54.[http://www.ncbi.nlm.nih.gov/pubmed/26527726 pubmed]

==2015 (14)==
*51. Hwang S*, Kim E*, '''Lee I**''', Marcotte EM**, Systematic comparison of variant calling pipelines using gold standard personal exome variants, '''''Scientific Reports''''' 2015 Dec 5:17875 [http://www.ncbi.nlm.nih.gov/pubmed/?term=26639839 pubmed]
*50. Shin J*, '''Lee I**''', Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling, '''''Plos One''''' 2015 Sep 22;10(9):e0139006 [http://www.ncbi.nlm.nih.gov/pubmed/26394049 pubmed]
*49. Shim JE*, '''Lee I**''', Network-assisted approaches for human disease research, '''''Animal Cells and Systems''''' 2015 Aug 19(4):231-235 [http://www.tandfonline.com/doi/abs/10.1080/19768354.2015.1074108 Link] [[media:19768354.2015.1074108.pdf|pdf]]
*48. Lee T*, Oh T, Yang S, Shin J, Hwang S, Kim CY, Kim H, Shim H, Shim JE, Ronald PC**, '''Lee I**''', RiceNet v2: an improved network prioritization server for rice genes, '''''Nucleic Acids Research''''' 2015 Jul 1;43(W1):W122-7 [http://www.ncbi.nlm.nih.gov/pubmed/25813048 pubmed]
*47. Shin J*, Yang S, Kim E, Kim CY, Shim H, Cho A, Kim H, Hwang S, Shim JE, '''Lee I**''', FlyNet: a versatile network prioritization server for the Drosophila community, '''''Nucleic Acids Research''''' 2015 Jul 1;43(W1):W91-7 [http://www.ncbi.nlm.nih.gov/pubmed/25943544 pubmed]
*46. Shim JE*, Hwang S, '''Lee I**''', Pathway-Dependent Effectiveness of Network Algorithms for Gene Prioritization, '''''PLoS One''''' 2015 Jun 19;10(6):e0130589. [http://www.ncbi.nlm.nih.gov/pubmed/26091506 pubmed]
*45. Han H*, Shim H, Shin D, Shim JE, Ko Y, Shin J, Kim H, Cho A, Kim E, Lee T, Kim H, Kim K, Yang S, Bae D, Yun A, Kim S, Kim CY, Cho HJ, Kang B, Shin S, '''Lee I**''', TRRUST: a reference database of human transcriptional regulatory interactions, '''''Scientific Reports''''' 2015 Jun 12;5:11432 [http://www.ncbi.nlm.nih.gov/pubmed/26066708 pubmed]
*44. '''Lee I**''', Mockler TC**, Editorial overview: Genome studies and molecular genetics: data-driven approaches to genotype-to-phenotype studies in crops, '''''Current Opinion in Plant Biology''''' 2015 Apr;24:iv-vi [http://www.ncbi.nlm.nih.gov/pubmed/25817324 pubmed]
*43. '''Lee I**''', Kim E, Marcotte EM**, Modes of Interaction between Individuals Dominate the Topologies of Real World Networks, '''''Plos One''''' 2015 Mar 20;10(3):e0121248 [http://www.ncbi.nlm.nih.gov/pubmed/25793969 Pubmed]
*42. Kim H*, Jung KW*, Maeng S, Chen YL, Shin J, Shim JE, Hwang S, Janbon G, Kim T, Heitman J, Bahn YS**, '''Lee I**''', Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans, '''''Scientific Reports''''' 2015 Mar 5;5:8767 [http://www.ncbi.nlm.nih.gov/pubmed/25739925 Pubmed] [http://f1000.com/prime/725377816?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
*41. Lee T*, Kim H, '''Lee I**''', Network-assisted crop systems genetics: network inference and integrative analysis, '''''Current Opinion in Plant Biology''''' 2015 Mar 5;5:8767. [http://www.ncbi.nlm.nih.gov/pubmed/25698380 Pubmed]
*40. Kim T*, Dreher K, Nilo-Poyanco R, '''Lee I''', Fiehn O, Lange BM, Nikolau BJ, Sumner L, Welti R, Wurtele ES, Rhee SY**, Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis thaliana using a genome-scale metabolic network, '''''Plant Physiology''''' 2015 Apr;167(4):1685-98 [http://www.ncbi.nlm.nih.gov/pubmed/25670818 Pubmed]
*39. Kim H*, Shim JE, Shin J, '''Lee I**''', EcoliNet: a database of cofunctional gene network for Escherichia coli, '''''Database''''' 2015 Feb 2;2015:bav001 [http://www.ncbi.nlm.nih.gov/pubmed/25650278 Pubmed]
*38. Lee T*, Yang S, Kim E, Ko Y, Hwang S, Shin J, Shim JE, Shim H, Kim H, Kim C, '''Lee I**''', AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species, '''''Nucleic Acids Research''''' 2015 Jan;43(Database issue):D996-1002 [http://www.ncbi.nlm.nih.gov/pubmed/25355510 Pubmed]

==2014 (5)-Sabbatical leave==
*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]
*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]
*35. Cho A*, Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
*34. Shin J*, Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
*33. Kim H*, Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]

==2013 (2)==
*32. Kim E*, Kim H, '''Lee I**''', JiffyNet: a web-based instant protein network modeler for newly sequenced species. '''''Nucleic Acids Research''''' 2013 Jul;41(Web Server issue):W192-7 [http://www.ncbi.nlm.nih.gov/pubmed/23685435 Pubmed][http://nar.oxfordjournals.org/content/early/2013/05/17/nar.gkt419.full.pdf+html pdf]
*31. '''Lee I**''' , Network approaches to the genetic dissection of phenotypes in animals and humans. '''''Animal Cells and Systems''''' 2013 17(2)75-79 [http://www.tandfonline.com/doi/abs/10.1080/19768354.2013.789076 Link]

==2012 (3)==
*30. Wang PI*, Hwang S*, Kincaid RP, Sullivan CS, '''Lee I**''', Marcotte EM**. RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. '''''Genome Biology''''' 2012 Dec 26;13(12):R125 [http://www.ncbi.nlm.nih.gov/pubmed/23268829 pubmed]
*29. Chae L**, '''Lee I**''', Shin J, Rhee SY**. Towards understanding how molecular networks evolve in plant. '''''Current Opinion in Plant Biology''''' 2012 Apr;15(2):177-84 [http://www.ncbi.nlm.nih.gov/pubmed/22280840 pubmed] [[media:CurrOpinPlantBiol 15-177.pdf|pdf]]
*28. Quanbeck SM1*, Brachova L, Campbell AA, Guan X, Perera A, He K, Rhee SY, Bais P, Dickerson JA, Dixon P, Wohlgemuth G, Fiehn O, Barkan L, Lange I, Lange BM, '''Lee I''', Cortes D, Salazar C, Shuman J, Shulaev V, Huhman DV, Sumner LW, Roth MR, Welti R, Ilarslan H, Wurtele ES, Nikolau BJ**. Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of “unknown function”. '''''Frontiers in Plant Science''''' 2012 Feb 10;3:15 [http://www.ncbi.nlm.nih.gov/pubmed/22645570/ pubmed][[media:Fpls-03-00015.pdf|pdf]]

==2011 (5)==
*27.'''Lee I**''', Seo YS, Coltrane D, Hwang S, Oh T, Marcotte EM**, Ronald PC**. Genetic dissection of the biotic stress response using a genome-scale gene network for rice. '''''PNAS''''' 2011 Nov 8;108(45):18548-53 [http://www.ncbi.nlm.nih.gov/pubmed/22042862 pubmed] [[media:PNAS-2011-Lee-18548-53.pdf|pdf]]
*26. Hwang S*, Rhee SY**, Marcotte EM**, '''Lee I**'''. Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana. '''''Nature Protocols''''' 2011 Aug 25;6(9):1429-42 [http://www.ncbi.nlm.nih.gov/pubmed/21886106 pubmed][[media:2011.08.25.online.nprot.2011.372.pdf|pdf]]
*25. '''Lee I**''' , Probabilistic functional gene societies. '''''Progress in Biophysics and Molecular Biology''''' 2011 Aug;106(2):435-42 [http://www.ncbi.nlm.nih.gov/pubmed/21281658 pubmed] [[media:Publications_023_n.pdf|pdf]]
*24. '''Lee I**''', Blom UM*, Wang PI, Shim JE, Marcotte EM**. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. '''''Genome Research''''' 2011 Jul;21(7):1109-21 [http://www.ncbi.nlm.nih.gov/pubmed/21536720 pubmed] [[media:Publications_025_n.pdf|pdf]]
*23. Seo YS*, Chern M, Bartley LE, Han M, Jung KH, '''Lee I''', Walia H, Richter T, Xu X, Cao P, Bai W, Ramanan R, Amonpant F, Arul L, Canlas PE, Ruan R, Park CJ, Chen X, Hwang S, Jeon JS, Ronald PC**. Towards establishment of a rice stress response interactome. '''''PLoS Genetics''''' 2011 Apr;7(4):e1002020 [http://www.ncbi.nlm.nih.gov/pubmed/21533176 pubmed] [[media:Publications_024.pdf|pdf]]

==2010 (4)==
*22. Huang N*, '''Lee I''', Marcotte EM, Hurles ME**. Characterising and predicting haploinsufficiency in the human genome, '''''PLoS Genet.''''' 2010 Oct 14;6(10):e1001154 [http://www.ncbi.nlm.nih.gov/pubmed/20976243 pubmed] [[media:Publications_022.pdf|pdf]]
*21. Kim E*, Shin J, '''Lee I**'''. Assessment of effectiveness of the network-guided genetic screen, '''''Mol Biosyst.''''' 2010 Oct;6(10):1803-6 [http://www.ncbi.nlm.nih.gov/pubmed/20697632 pubmed] [[media:Publications_021.pdf|pdf]]
*20. '''Lee I**''', Lehner B**, Vavouri T, Shin J, Fraser AG**, Marcotte EM**. Andrew G. Fraser, and Edward M. Marcotte, Predicting genetic modifier loci using functional gene networks, '''''Genome Research''''' 2010 Aug;20(8):1143-53 ''co-corresponding author'' [http://www.ncbi.nlm.nih.gov/pubmed/20538624 pubmed] [[media:Publications_020.pdf|pdf]]
*19. '''Lee I**''', Ambaru B, Thakkar P, Marcotte EM**, Rhee SY**. Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana '''''Nature Biotechnology''''', 2010 Feb;28(2):149-56 ''co-corresponding author'' [http://www.ncbi.nlm.nih.gov/pubmed/20118918 pubmed] [[media:Publications_019.pdf|pdf]]

==2009 (3)==
*18. '''Lee I*''', Marcotte EM**. 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. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM**. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
*16. Gray RS*, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM**, Wallingford JB**, Finnell RH**. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
*14. '''Lee I*''', Marcotte EM**. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG**, Marcotte EM**. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] 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)

==Before 2007 (12)==
*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]]
*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]]
*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]]
*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]]
*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]]
*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]]
*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)
*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)
*4. '''Insuk Lee*''' and Rasika Harshey**. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
*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)
*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)
*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)

Publications

2017-08-16T01:48:50Z

Cykim: /* 2015 (14) */

* [http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
* [http://www.researcherid.com/rid/F-7722-2010 {{#widget:AddHtml|content=<img src='https://labs.researcherid.com/mashlets/badge/rid-idsymbol4.gif' border='0' />}}]
* '*' First authors; '**' Corresponding authors;
==2017 (9)==
*70. Lee T*, Hwang S*, Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
*69. Lee T*, '''Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
*68. Shim JE*, Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 Apr 26; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
*67. Kim E*, '''Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
*66. Shim JE*, Lee T*, '''Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [http://www.tandfonline.com/doi/full/10.1080/19768354.2017.1284156 article link]
*65. Kim H*, Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
*64. Jang K*, Kim K, Cho A, '''Lee I''', Choi JK**, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]

==2016 (10)==
*61. Shin J**, '''Lee I**''', Construction of Functional Gene Networks Using Phylogenetic Profiles. '''''Methods in Molecular Biology''''' 2016 Nov 29; 1526:87-98 [http://www.ncbi.nlm.nih.gov/pubmed/27896737 pubmed]
*60. Shim H*, Kim JH*, Kim CY*, Hwang S, Kim H, Yang S, Lee JE**, '''Lee I**''', Function-driven discovery of disease genes in zebraﬁsh using an integrated genomics big data resource,'''''Nucleic Acids Research''''' 2016 Nov 16;44(20):9611-9623 [http://www.ncbi.nlm.nih.gov/pubmed/27903883 pubmed]
*59. Shim JE*, '''Lee I**''' Weighted mutual information analysis substantially improves domain-based functional network models. '''''Bioinformatics''''' 2016 Sep 15;32(18):2824-30 [http://www.ncbi.nlm.nih.gov/pubmed/27207946 pubmed]
*58. Lee JY*, Kim E*, Choi SM, Kim DW, Kim KP, '''Lee I**''', Kim HS** Microvesicles from brain-extract—treated mesenchymal stem cells improve neurological functions in a rat model of ischemic stroke. '''''Scientific Reports''''' 2016 Sep 9; 6:33038 [http://www.ncbi.nlm.nih.gov/pubmed/27609711 pubmed]
*57. Kim SM*, Kim JW, Kwak TH, Park SW, Kim KP, Park H, Lim KT, Kang K, Kim J, Yang JH, Han H, '''Lee I''', Hyun JK, Bae YM, Schöler HR, Lee HT, Han DW** Generation of Integration-free Induced Neural Stem Cells from Mouse Fibroblasts. '''''J Biol Chem'''''. 2016 Jul 1. 291(27):14199-212. [http://www.ncbi.nlm.nih.gov/pubmed/27189941 pubmed]
*56. Cho A*, Shim JE, Kim E, Supek F, Lehner B**, '''Lee I**'''. MUFFINN: cancer gene discovery via network analysis of somatic mutation data. '''''Genome Biology''''' 2016 June 23;17(1):129 [http://www.ncbi.nlm.nih.gov/pubmed/27333808 pubmed]
*55. Hwang S*, Kim CY*, Ji SG, Go J, Kim H, Yang S, Kim HJ, Cho A, Yoon SS**, '''Lee I**'''. Network-assisted investigation of virulence and antibiotic-resistance systems in Pseudomonas aeruginosa.'''''Scientific Reports''''' 2016 May 19; 6:26223. [http://www.ncbi.nlm.nih.gov/pubmed/27194047 pubmed]
*54. Yoon MY*, Min KB, Lee KM, Yoon Y, Kim Y, Oh YT, Lee K, Chun J, Kim BY, Yoon SH, '''Lee I''', Kim CY, Yoon SS**,. A single gene of a commensal microbe affects host susceptibility to enteric infection.'''''Nature Communications''''' 2016 May 13; 7:11606. [http://www.ncbi.nlm.nih.gov/pubmed/27173141 pubmed]
*53. Jo J*, Hwang S*, Kim HJ*, Hong S, Lee JE, Lee SG, Baek A, Han H, Lee JI, '''Lee I**''', Lee DR**. An integrated systems biology approach identifies positive cofactor 4 as a factor that increases reprogramming efficiency.'''''Nucleic Acids Research''''' 2016 Feb 18; 44(3):1203-15.[http://www.ncbi.nlm.nih.gov/pubmed/26740582 pubmed]
*52. Kim E*, Hwang S, Kim H, Shim H, Kang B, Yang S, Shim JH, Shin SY, Marcotte EM, '''Lee I**'''. MouseNet v2: A database of gene networks for studying the laboratory mouse and eight other model vertebrates,'''''Nucleic Acids Research''''' 2016 Jan 4;44(D1):D848-54.[http://www.ncbi.nlm.nih.gov/pubmed/26527726 pubmed]

==2015 (14)==
*51. Hwang S*, Kim E*, '''Lee I**''', Marcotte EM**, Systematic comparison of variant calling pipelines using gold standard personal exome variants, '''''Scientific Reports''''' 2015 Dec 5:17875 [http://www.ncbi.nlm.nih.gov/pubmed/?term=26639839 pubmed]
*50. Shin J*, '''Lee I**''', Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling, '''''Plos One''''' 2015 Sep 22;10(9):e0139006 [http://www.ncbi.nlm.nih.gov/pubmed/26394049 pubmed]
*49. Shim JE*, '''Lee I**''', Network-assisted approaches for human disease research, '''''Animal Cells and Systems''''' 2015 Aug 19(4):231-235 [http://www.tandfonline.com/doi/abs/10.1080/19768354.2015.1074108 Link] [[media:19768354.2015.1074108.pdf|pdf]]
*48. Lee T*, Oh T, Yang S, Shin J, Hwang S, Kim CY, Kim H, Shim H, Shim JE, Ronald PC**, '''Lee I**''', RiceNet v2: an improved network prioritization server for rice genes, '''''Nucleic Acids Research''''' 2015 Jul 1;43(W1):W122-7 [http://www.ncbi.nlm.nih.gov/pubmed/25813048 pubmed]
*47. Shin J*, Yang S, Kim E, Kim CY, Shim H, Cho A, Kim H, Hwang S, Shim JE, '''Lee I**''', FlyNet: a versatile network prioritization server for the Drosophila community, '''''Nucleic Acids Research''''' 2015 Jul 1;43(W1):W91-7 [http://www.ncbi.nlm.nih.gov/pubmed/25943544 pubmed]
*46. Shim JE*, Hwang S, '''Lee I**''', Pathway-Dependent Effectiveness of Network Algorithms for Gene Prioritization, '''''PLoS One''''' 2015 Jun 19;10(6):e0130589. [http://www.ncbi.nlm.nih.gov/pubmed/26091506 pubmed]
*45. Han H*, Shim H, Shin D, Shim JE, Ko Y, Shin J, Kim H, Cho A, Kim E, Lee T, Kim H, Kim K, Yang S, Bae D, Yun A, Kim S, Kim CY, Cho HJ, Kang B, Shin S, '''Lee I**''', TRRUST: a reference database of human transcriptional regulatory interactions, '''''Scientific Reports''''' 2015 Jun 12;5:11432 [http://www.ncbi.nlm.nih.gov/pubmed/26066708 pubmed]
*44. '''Lee I**''', Mockler TC**, Editorial overview: Genome studies and molecular genetics: data-driven approaches to genotype-to-phenotype studies in crops, '''''Current Opinion in Plant Biology''''' 2015 Apr;24:iv-vi [http://www.ncbi.nlm.nih.gov/pubmed/25817324 pubmed]
*43. '''Lee I**''', Kim E, Marcotte EM**, Modes of Interaction between Individuals Dominate the Topologies of Real World Networks, '''''Plos One''''' 2015 Mar 20;10(3):e0121248 [http://www.ncbi.nlm.nih.gov/pubmed/25793969 Pubmed]
*42. Kim H*, Jung KW*, Maeng S, Chen YL, Shin J, Shim JE, Hwang S, Janbon G, Kim T, Heitman J, Bahn YS**, '''Lee I**''', Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans, '''''Scientific Reports''''' 2015 Mar 5;5:8767 [http://www.ncbi.nlm.nih.gov/pubmed/25739925 Pubmed] This paper was recommended by Faculty of 1000 Biology. [http://f1000.com/prime/725377816?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
*41. Lee T*, Kim H, '''Lee I**''', Network-assisted crop systems genetics: network inference and integrative analysis, '''''Current Opinion in Plant Biology''''' 2015 Mar 5;5:8767. [http://www.ncbi.nlm.nih.gov/pubmed/25698380 Pubmed]
*40. Kim T*, Dreher K, Nilo-Poyanco R, '''Lee I''', Fiehn O, Lange BM, Nikolau BJ, Sumner L, Welti R, Wurtele ES, Rhee SY**, Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis thaliana using a genome-scale metabolic network, '''''Plant Physiology''''' 2015 Apr;167(4):1685-98 [http://www.ncbi.nlm.nih.gov/pubmed/25670818 Pubmed]
*39. Kim H*, Shim JE, Shin J, '''Lee I**''', EcoliNet: a database of cofunctional gene network for Escherichia coli, '''''Database''''' 2015 Feb 2;2015:bav001 [http://www.ncbi.nlm.nih.gov/pubmed/25650278 Pubmed]
*38. Lee T*, Yang S, Kim E, Ko Y, Hwang S, Shin J, Shim JE, Shim H, Kim H, Kim C, '''Lee I**''', AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species, '''''Nucleic Acids Research''''' 2015 Jan;43(Database issue):D996-1002 [http://www.ncbi.nlm.nih.gov/pubmed/25355510 Pubmed]

==2014 (5)-Sabbatical leave==
*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]
*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]
*35. Cho A*, Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
*34. Shin J*, Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
*33. Kim H*, Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]

==2013 (2)==
*32. Kim E*, Kim H, '''Lee I**''', JiffyNet: a web-based instant protein network modeler for newly sequenced species. '''''Nucleic Acids Research''''' 2013 Jul;41(Web Server issue):W192-7 [http://www.ncbi.nlm.nih.gov/pubmed/23685435 Pubmed][http://nar.oxfordjournals.org/content/early/2013/05/17/nar.gkt419.full.pdf+html pdf]
*31. '''Lee I**''' , Network approaches to the genetic dissection of phenotypes in animals and humans. '''''Animal Cells and Systems''''' 2013 17(2)75-79 [http://www.tandfonline.com/doi/abs/10.1080/19768354.2013.789076 Link]

==2012 (3)==
*30. Wang PI*, Hwang S*, Kincaid RP, Sullivan CS, '''Lee I**''', Marcotte EM**. RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. '''''Genome Biology''''' 2012 Dec 26;13(12):R125 [http://www.ncbi.nlm.nih.gov/pubmed/23268829 pubmed]
*29. Chae L**, '''Lee I**''', Shin J, Rhee SY**. Towards understanding how molecular networks evolve in plant. '''''Current Opinion in Plant Biology''''' 2012 Apr;15(2):177-84 [http://www.ncbi.nlm.nih.gov/pubmed/22280840 pubmed] [[media:CurrOpinPlantBiol 15-177.pdf|pdf]]
*28. Quanbeck SM1*, Brachova L, Campbell AA, Guan X, Perera A, He K, Rhee SY, Bais P, Dickerson JA, Dixon P, Wohlgemuth G, Fiehn O, Barkan L, Lange I, Lange BM, '''Lee I''', Cortes D, Salazar C, Shuman J, Shulaev V, Huhman DV, Sumner LW, Roth MR, Welti R, Ilarslan H, Wurtele ES, Nikolau BJ**. Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of “unknown function”. '''''Frontiers in Plant Science''''' 2012 Feb 10;3:15 [http://www.ncbi.nlm.nih.gov/pubmed/22645570/ pubmed][[media:Fpls-03-00015.pdf|pdf]]

==2011 (5)==
*27.'''Lee I**''', Seo YS, Coltrane D, Hwang S, Oh T, Marcotte EM**, Ronald PC**. Genetic dissection of the biotic stress response using a genome-scale gene network for rice. '''''PNAS''''' 2011 Nov 8;108(45):18548-53 [http://www.ncbi.nlm.nih.gov/pubmed/22042862 pubmed] [[media:PNAS-2011-Lee-18548-53.pdf|pdf]]
*26. Hwang S*, Rhee SY**, Marcotte EM**, '''Lee I**'''. Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana. '''''Nature Protocols''''' 2011 Aug 25;6(9):1429-42 [http://www.ncbi.nlm.nih.gov/pubmed/21886106 pubmed][[media:2011.08.25.online.nprot.2011.372.pdf|pdf]]
*25. '''Lee I**''' , Probabilistic functional gene societies. '''''Progress in Biophysics and Molecular Biology''''' 2011 Aug;106(2):435-42 [http://www.ncbi.nlm.nih.gov/pubmed/21281658 pubmed] [[media:Publications_023_n.pdf|pdf]]
*24. '''Lee I**''', Blom UM*, Wang PI, Shim JE, Marcotte EM**. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. '''''Genome Research''''' 2011 Jul;21(7):1109-21 [http://www.ncbi.nlm.nih.gov/pubmed/21536720 pubmed] [[media:Publications_025_n.pdf|pdf]]
*23. Seo YS*, Chern M, Bartley LE, Han M, Jung KH, '''Lee I''', Walia H, Richter T, Xu X, Cao P, Bai W, Ramanan R, Amonpant F, Arul L, Canlas PE, Ruan R, Park CJ, Chen X, Hwang S, Jeon JS, Ronald PC**. Towards establishment of a rice stress response interactome. '''''PLoS Genetics''''' 2011 Apr;7(4):e1002020 [http://www.ncbi.nlm.nih.gov/pubmed/21533176 pubmed] [[media:Publications_024.pdf|pdf]]

==2010 (4)==
*22. Huang N*, '''Lee I''', Marcotte EM, Hurles ME**. Characterising and predicting haploinsufficiency in the human genome, '''''PLoS Genet.''''' 2010 Oct 14;6(10):e1001154 [http://www.ncbi.nlm.nih.gov/pubmed/20976243 pubmed] [[media:Publications_022.pdf|pdf]]
*21. Kim E*, Shin J, '''Lee I**'''. Assessment of effectiveness of the network-guided genetic screen, '''''Mol Biosyst.''''' 2010 Oct;6(10):1803-6 [http://www.ncbi.nlm.nih.gov/pubmed/20697632 pubmed] [[media:Publications_021.pdf|pdf]]
*20. '''Lee I**''', Lehner B**, Vavouri T, Shin J, Fraser AG**, Marcotte EM**. Andrew G. Fraser, and Edward M. Marcotte, Predicting genetic modifier loci using functional gene networks, '''''Genome Research''''' 2010 Aug;20(8):1143-53 ''co-corresponding author'' [http://www.ncbi.nlm.nih.gov/pubmed/20538624 pubmed] [[media:Publications_020.pdf|pdf]]
*19. '''Lee I**''', Ambaru B, Thakkar P, Marcotte EM**, Rhee SY**. Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana '''''Nature Biotechnology''''', 2010 Feb;28(2):149-56 ''co-corresponding author'' [http://www.ncbi.nlm.nih.gov/pubmed/20118918 pubmed] [[media:Publications_019.pdf|pdf]]

==2009 (3)==
*18. '''Lee I*''', Marcotte EM**. 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. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM**. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
*16. Gray RS*, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM**, Wallingford JB**, Finnell RH**. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
*14. '''Lee I*''', Marcotte EM**. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG**, Marcotte EM**. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] 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)

==Before 2007 (12)==
*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]]
*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]]
*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]]
*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]]
*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]]
*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]]
*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)
*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)
*4. '''Insuk Lee*''' and Rasika Harshey**. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
*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)
*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)
*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)

Software

2017-08-03T11:54:09Z

Cykim: /* Bacteria */

__NOTOC__
=='''Co-functional gene networks'''==

==''Human and Laboratory Animals''==
{|border="0" width="500"
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
|align="center"|[[file:danionet_logo.png|150px|link=http://www.inetbio.org/danionet]]
|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]
|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
|-
|align="center"|''Homo sapiens''
|align="center"|''Mus musculus''
|align="center"|''Danio rerio''
|align="center"|''Drosophila melanogaster''
|align="center"|''Caenorhabditis elegans''
|}

==''Plants''==
{|border="0" width="400"
|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]]
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=http://www.inetbio.org/maizenet]]
|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
|align="center"|[[File:WheatNet_logo.png|150px|link=http://www.inetbio.org/wheatnet]]
|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]
|align="center"|[[File:Tomatonet_logo.png|150px|link=http://www.inetbio.org/tomatonet]]
|-
|align="center"|''Arabidopsis thaliana''
|align="center"|''Zea mays''
|align="center"|''Oryza sativa''
|align="center"|''Triticum aestivum''
|align="center"|''Glycine max''
|align="center"|''Solanum lycopersicum''
|}

==''Fungi''==
{|border="0" width="200"
|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]]
|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]]
|-
|align="center"|''Saccharomyces cerevisiae''
|align="center"|''Cryptococcus neoformans''
|}

==''Bacteria''==
{|border="0" width="200"
|align="center"|[[File:Mrsanet.jpg|150px|link=http://www.inetbio.org/mrsanet]]
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]]
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
|align="center"|[[File:XooNet_logo.png|150px|link=http://www.inetbio.org/xoonet]]
|-
|align="center"|''Staphylococcus aureus''
|align="center"|''Pseudomonas aeruginosa''
|align="center"|''Escherichia coli''
|align="center"|''Xanthomonas oryzae pv. oryzae''
|}

==''Build your own co-functional networks''==
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]]
'''JiffyNet''': Instant gene network building server for newly sequenced species

=='''Transcriptional Regulatory Networks'''==
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST''': A reference database of TF-target interactions in human and mouse

=='''Network-based Disease Research Servers'''==
[[File:Coexpedia.png |150px|link=http://www.coexpedia.org]] '''COEXPEDIA''': Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)

[[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

[[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation data

[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN''': Network-assisted prediction of disease pathways in model organisms

[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only)

=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
[[WMI|<big>'''Project Page'''</big>]]