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Bioinformatics Lab - User contributions [en]
2024-03-29T01:24:41Z
User contributions
MediaWiki 1.20.5
https://netbiolab.org/w/Software
Software
2024-03-06T08:00:22Z
<p>Administrator: </p>
<hr />
<div>__NOTOC__<br />
=='''Microbiome Research'''==<br />
[[File:Hrgm logo.png|150px|link=//www.decodebiome.org/HRGM]]<br />
'''HRGM''': A Human Reference Gut Microbiome comprising 232,098 genomes for 5414 prokaryotic species and 103 million unique proteins<br />
<br />
[[File:mrgm_logo.png|150px|link=//www.decodebiome.org/MRGM]]<br />
'''MRGM''': A Mouse Reference Gut Microbiome comprising 46,267 genomes for 1,689 bacterial species and 15.2 million proteins<br />
<br />
=='''Single-cell Biology'''==<br />
[[File:ScHumanNet github banner.final.jpg|150px|link=https://github.com/netbiolab/scHumanNet]]<br />
'''scHumanNet''': Cell-type-specific functional gene networks using single-cell RNA-sequencing data<br />
<br />
[[File:VC_logo.png|150px|link=//www.grnpedia.org/cytometry]]<br />
'''VirtualCytometry''': A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.''<br />
<br />
<br />
=='''Network Medicine'''==<br />
[[File:HumanNet_logo_with_title.png|150px|link=//www.inetbio.org/humannet]]'''HumanNet''': Human gene networks for disease research<br />
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[[File:TRRUST_logo.jpg |150px|link=//www.grnpedia.org/trrust/]] '''TRRUST''': Curated TF-target interaction networks in human and mouse<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 />
[[File:Ngsea logo1.png |150px|link=//www.inetbio.org/ngsea/]] '''NGSEA''': Network-augmented gene set enrichment analysis tool<br />
<br />
[[File:Cover title muffinn.png |150px|link=//www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation data<br />
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[[File:GWAB_logo.png |150px|link=//www.inetbio.org/gwab]] '''GWAB''': A web server for network-based boosting of human genome-wide association data<br />
<br />
[[File:Logo morphin.png|150px|link=//www.inetbio.org/morphin/]] '''MORPHIN''': Network-assisted prediction of disease pathways in model organisms<br />
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[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only)<br />
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<br />
=='''Functional Gene Networks'''==<br />
<br />
==''Animals''==<br />
{|border="0" width="400"<br />
|align="center"|[[file:MouseNetLogo.png|150px|link=//www.inetbio.org/mousenet]]<br />
|align="center"|[[file:danionet_logo.png|150px|link=//www.inetbio.org/danionet]]<br />
|align="center"|[[file:Flynet.png|150px|link=//www.inetbio.org/flynet]]<br />
|align="center"|[[file:WormNetv3.jpg|150px|link=//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=//www.inetbio.org/aranet]]<br />
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=//www.inetbio.org/maizenet]]<br />
|align="center"|[[file:RiceNetv2 logo.png|150px|link=//www.inetbio.org/ricenet]]<br />
|align="center"|[[File:WheatNet_logo.png|150px|link=//www.inetbio.org/wheatnet]]<br />
|align="center"|[[File:BarleyNet_logo.png|150px|link=//www.inetbio.org/barleynet]]<br />
|align="center"|[[File:Soynetlogo.png|150px|link=//www.inetbio.org/soynet]]<br />
|align="center"|[[File:Tomatonet_logo.png|150px|link=//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"|''Hordeum vulgare''<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=//www.inetbio.org/yeastnet]]<br />
|align="center"|[[file:CryptoNet.png|150px|link=//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=//www.inetbio.org/pseudomonasnet]]<br />
|align="center"|[[File:Staphnet_logo.JPG|150px|link=//www.inetbio.org/staphnet]]<br />
|align="center"|[[File:KlebNet_logo.png|150px|link=//www.inetbio.org/klebnet]]<br />
|align="center"|[[File:EcoliNet.png|150px|link=//www.inetbio.org/ecolinet]]<br />
|align="center"|[[File:XooNet_logo.png|150px|link=//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 />
<br />
==''Build your own Functional gene networks''==<br />
[[File:BiomeNet_logo.png | 150px | link=http://kobic.re.kr/biomenet]]<br />
'''BiomeNet''': A database for construction and analysis of functional interaction networks for any species with a sequenced genome<br />
<br />
<br />
=='''Network-augmented GWAS Analysis for Arabidopsis'''==<br />
[[File:araGWAB_logo.png|150px|link=//www.inetbio.org/aragwab]]<br />
'''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana''<br />
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=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==<br />
[[WMI|<big>'''Project Page'''</big>]]<br />
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<br />
=='''Domain2Pathway by Pathway Specificity (PS) '''==<br />
[[PS|<big>'''Project Page'''</big>]]</div>
Administrator
https://netbiolab.org/w/Teaching
Teaching
2021-09-24T07:00:38Z
<p>Administrator: </p>
<hr />
<div>== Teaching materials for Experiment in microbiology and biochemical engineering laboratory Course ==<br />
[//netbiolab.org/wiki/images/1/18/2018_NBLexperiment_training_material.zip 2020 netbiolab experiment teaching material]<br />
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[//netbiolab.org/wiki/images/8/8e/2019_nbl_experiment.pdf 2019 netbiolab experiment teaching material (pdf)]<br />
<br />
== Teaching materials for Yonsei Bioinformatics Course ==<br />
[//netbiolab.org/wiki/teaching_materials/Bioinformatics_Machine_Learning_Practice_2021.zip 2021 Bioinformatics Machine Learning Practice]<br />
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[//netbiolab.org/wiki/images/b/b1/2020_1_Tensorflow.zip 2020 Bioinformatics Deep Learning Practice (Tensorflow)]<br />
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[//netbiolab.org/wiki/teaching_materials/2019_1_Kallisto_material.zip 2019 Bioinformatics Kallisto Practice]<br />
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[//netbiolab.org/wiki/teaching_materials/2019_1_WebMEV_material.zip 2019 Bioinformatics WebMeV Practice]<br />
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<br />
== Teaching materials for BIML workshop ==<br />
<br />
[//netbiolab.org/wiki/images/0/0e/BIML2020_Lecture_Files.zip BIMIL2020 scGRN & scATAC lecture files]<br />
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[//netbiolab.org/wiki/images/7/7b/2017_BIML_0216_2.zip BIML2017 practice 2 PPT file & python scripts]<br />
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[//netbiolab.org/wiki/images/4/4b/Practice1.pdf BIML2016 practice 1 PPT file]<br />
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[//netbiolab.org/wiki/images/c/c0/Biml_python_scripts.zip BIML2016 practice 2 python scripts]<br />
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<div>{{#widget:AddHtml|content=<img src="../wiki/wordcloud_2018_2020.jpg" title="Research Keyword Cloud (2018-2020)" />}}</div></div>
Administrator
https://netbiolab.org/w/Publications
Publications
2021-09-24T00:55:29Z
<p>Administrator: </p>
<hr />
<div>*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]<br />
*[https://www.ibric.org/hanbitsa/treatise_index_for_author.php?Page=1&idauthorid=760 BRIC 한빛사논문]<br />
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]<br />
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]<br />
* '*' First authors; '**' Corresponding authors; <br />
==2021==<br />
*96. '''Jae-Won Cho*''', Hyo Sup Shim, Chang Young Lee, Seong Yong Park, Min Hee Hong, '''Insuk Lee**, Hye Ryun Kim**''' The importance of enhancer methylation for epigenetic regulation of tumorigenesis in squamous lung cancer. [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]<br />
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*95. '''Chan Yeong Kim*, Muyoung Lee*''', Sunmo Yang, Kyungnam Kim, Dongeun Yong, Hye Ryun Kim, '''Insuk Lee''' Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes '''''Genome Medicine''''' 2021 Aug 27;13(1):13 [https://pubmed.ncbi.nlm.nih.gov/34446072/ pubmed] [https://www.biorxiv.org/content/10.1101/2020.11.09.375873v1 '''''bioRxiv preprint'''''] <br />
<br><br />
*94. Ho-Seok Lee, Ilyeong Choi, Young Jeon, Hee-Kyung Ahn, Huikyong Cho, JiWoo Kim, Jae-Hee Kim, Jung-Min Lee, SungHee Lee, Julian Bünting, Dong Hye Seo, '''Tak Lee''', Du-Hwa Lee, '''Insuk Lee''', Man-Ho Oh, Tae-Wuk Kim, Youssef Belkhadir, Hyun-Sook Pai Chaperone-like protein DAY plays critical roles in photomorphogenesis '''''Nature Communications''''' 2021 Jul 7;12(1):4194 [https://https://pubmed.ncbi.nlm.nih.gov/34234144/ pubmed] <br />
<br><br />
*93. '''Jae-Won Cho*''', Jimin Son*, Sang-Jun Ha**, '''Insuk Lee**''', Systems biology analysis identifies TNFRSF9 as a functional marker of tumor-infiltrating regulatory T-cell enabling clinical outcome prediction in lung cancer '''''Computational and Structural Biotechnology Journal''''' 2021 Jan 21; 19:860-868 [https://pubmed.ncbi.nlm.nih.gov/33598101 pubmed] <br />
<br><br />
*92. '''Tak Lee*''', '''Insuk Lee**''' Genome-wide Association Studies in Arabidopsis thaliana: Statistical Analysis and Network-Based Augmentation of Signals '''''Methods in Molecular Biology''''' 2020 Nov; 2200:187-210 [https://pubmed.ncbi.nlm.nih.gov/33175379 pubmed] [https://netbiolab.org/wiki/glucose_germrate.txt Supplementary File 1] [https://netbiolab.org/wiki/glucose_sig_accessions.txt Supplementary File 2]<br />
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==2020 (9)== <br />
*91. '''Junha Cha*''', '''Insuk Lee**''' Single-cell Network Biology for Resolving Cellular Heterogeneity in Human Diseases '''''Experimental & Molecular Medicine''''' 2020 Nov;52(11):1798-1808 [https://pubmed.ncbi.nlm.nih.gov/33244151 pubmed]<br />
<br><br />
*90. Jimin Son*, '''Jae-Won Cho*''', Hyo Jin Park, Jihyun Moon, Seyeon Park, Hoyoung Lee, Jeewon Lee, Ga min Kim, Su-Myeong Park, Sergio A. Lira, Andrew N. Mckenzie, Hye Young Kim, Cheol Yong Choi, Yong Taik Lim, Seong Yong Park, Hye Ryun Kim, Su-Hyung Park, Eui-Cheol Shin, '''Insuk Lee'''** & Sang-Jun Ha**, Tumor-Infiltrating Regulatory T Cell Accumulation in the Tumor Microenvironment is Mediated by IL33/ST2 Signaling '''''Cancer Immunology Research''''' 2020 Nov; 8(11):1393-1406 [https://pubmed.ncbi.nlm.nih.gov/32878747 pubmed] '''Spotlighted''' by [https://acir.org/journal-articles/cancer-immunobiology/immune-cell-biology?entryId=26357 Accelerating Cancer Immunotherapy Research]<br />
<br><br />
*89. '''Jae-Won Cho*''', Min Hee Hong, Sang-Jun Ha, Young-Joon Kim, Byoung Chul Cho, '''Insuk Lee**''', and Hye Ryun Kim** Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer [https://netbiolab.org/wiki/Supplementary_Table_S1-6.zip Supplementary File] '''''Experimental & Molecular Medicine''''' 2020 Sep 02;52(9):1550-1563 [https://pubmed.ncbi.nlm.nih.gov/32879421 pubmed]<br />
<br><br />
*88. '''Seungbyn Baek*''', '''Insuk Lee**''' Single-cell ATAC sequencing analysis: from data preprocessing to hypothesis generation '''''Computational and Structural Biotechnology Journal''''' 2020 June 28;18:1429-1439 [https://pubmed.ncbi.nlm.nih.gov/32637041 pubmed]<br />
<br><br />
*87. '''Eiru Kim*, Dasom Bae*, Sunmo Yang*''', Gunhwan Ko, Sungho Lee, Byungwook Lee**, '''Insuk Lee**'''. BiomeNet: A database for construction and analysis of functional interaction networks for any species with a sequenced genome '''''Bioinformatics''''' 2020 Mar 1:36(5):1584-1589 [https://www.ncbi.nlm.nih.gov/pubmed/31599923 pubmed]<br />
<br><br />
*86. '''Kyungsoo Kim*''', Seyeon Park*, Seong Yong Park, Gamin Kim, Su Myeong Park, Jae-Won Cho, Da Hee Kim, Young Min Park, Yoon Woo Koh, Hye Ryun Kim, Sang-Jun Ha** and '''Insuk Lee**''', Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer '''''Genome Medicine''''' 2020 Feb 28;12:22 [https://pubmed.ncbi.nlm.nih.gov/32111241 pubmed]<br />
<br><br />
*85. '''Sungho Lee*, Tak Lee*''', Sunmo Yang and '''Insuk Lee**''', BarleyNet: a network-based functional omics analysis server for cultivated barley, Hordeum vulgare L. '''''Frontiers in Plant Science''''' 2020 Feb 18;11:98 [https://pubmed.ncbi.nlm.nih.gov/32133024/ pubmed]<br />
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*84. '''Kyungsoo Kim*''', Sunmo Yang, Sang-Jun Ha, '''Insuk Lee**''', VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data '''''Bioinformatics''''' 2020 Jan 15;36(2):546-551 [https://www.ncbi.nlm.nih.gov/pubmed/31373613 pubmed]<br />
<br><br />
*83. '''Jung Eun Shim*, Insuk Lee**''', Construction of functional protein networks using domain profile associations, '''''Methods in Molecular Biology''''' 2020 Jan;2074:35-44 [https://www.ncbi.nlm.nih.gov/pubmed/31583628 pubmed]<br />
<br><br />
<br />
==2019 (6)== <br />
*82. '''Han H*''', Lee S, '''Lee I**''', NGSEA: network-based gene set enrichment analysis for interpreting gene expression phenotypes with functional gene sets '''''Mol Cells''''' 2019 Aug 31;42(8):579-588. [https://www.ncbi.nlm.nih.gov/pubmed/31307154 pubmed]<br />
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*81. '''Lee T*, Lee S*''', Yang S, '''Lee I**'''. MaizeNet: A co-functional network for network-assisted systems genetics in Zea mays '''''The Plant Journal''''' 2019 Aug 99(3):571-582 [https://www.ncbi.nlm.nih.gov/pubmed/31006149 pubmed]<br />
<br><br />
*80. '''Lee M*''', Pinto NA*, Kim CY, Yang S, D'Souza R, Yong D**, Lee I**. Network integrative genomic and transcriptomic analysis of carbapenem-resistant Klebsiella pneumoniae strains identifies genes for antibiotic-resistance and virulence '''''mSystems''''' 2019 Aug;4(4):e00202-19. [https://www.ncbi.nlm.nih.gov/pubmed/31117026 pubmed] <br />
<br><br />
*79. '''Shim JE*''', Kim JH, Shin J, Lee JE, '''Lee I**''' Pathway-specific protein domains are predictive for human diseases '''''PLOS Computational Biology''''' 2019 May 10;15(5):e1007052 [https://www.ncbi.nlm.nih.gov/pubmed/31075101 pubmed] <br />
<br><br />
*78. '''Kim H*''', Joe A*, Lee M, Yang S, Ma X, Ronald PC**, '''Lee I**'''. A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems '''''Mol Cells''''' 2019 Feb 28;42(2):166-174 [https://www.ncbi.nlm.nih.gov/pubmed/30759970 pubmed]<br />
<br><br />
*77. '''Hwang S*, Kim CY*''', Yang S, Kim E, Hart T, Marcotte EM, '''Lee I**'''. HumanNet v2: human gene networks for disease research '''''Nucleic Acids Research''''' 2019 Jan 8;47(D1):D573–D580.[https://www.ncbi.nlm.nih.gov/pubmed/30418591 pubmed]<br />
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<br />
==2018 (5)== <br />
*76. '''Han H*''', Lehner B, '''Lee I**''', Cancer gene discovery by network analysis of somatic mutations using the MUFFINN server, '''''Methods in Molecular Biology''''' 2018 Dec 13; 1907:37-50.[https://www.ncbi.nlm.nih.gov/pubmed/30542989 pubmed]<br />
<br><br />
*75. '''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. [https://www.ncbi.nlm.nih.gov/pubmed/30018396 pubmed]<br />
<br><br />
*74. Lim KT, Kim J, Hwang SI, Zhang L, Han H, Bae D, Kim KP, Hu YP, Schöler HR, '''Lee I''', Hui L, Han DW, Direct Conversion of Mouse Fibroblasts into Cholangiocyte Progenitor Cells. '''''Stem Cell Reports''''' 2018 Mar 27. 10:1-15.[https://www.ncbi.nlm.nih.gov/pubmed/29606616 pubmed]<br />
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*73. '''Lee T*, Lee I**''', araGWAB: A web application for network-based boosting of genome-wide association signals in Arabidopsis '''''Scientific Reports''''' 2018 Feb 13;8(1):2925.[https://www.ncbi.nlm.nih.gov/pubmed/29440686 pubmed]<br />
<br><br />
*72. '''Han H*''', Cho JW, Lee S, Yun A, Kim H, Bae D, Yang S, Kim CY, Lee M, Kim E, Lee S, Kang B, Jeong D, Kim Y, Jeon HN, Jung H, Nam S, Chung M, Kim JH, '''Lee I**''', TRRUST v2: An expanded reference database of human and mouse transcriptional regulatory interactions '''''Nucleic Acids Research''''' 2018 Jan 4;46(D1):D380–D386.[https://www.ncbi.nlm.nih.gov/pubmed/29087512 pubmed]<br />
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==2017 (10)== <br />
*71. '''Kim CY*, Lee I**''', Functional gene networks based on the gene neighborhood in metagenomes, '''''Animal Cells and Systems''''' 2017 Sept 29; 21:301-306; <br />
<br><br />
*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] <br />
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*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]<br />
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*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 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]<br />
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*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 />}}]<br />
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*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; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]<br />
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*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]<br />
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*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]<br />
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*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]<br />
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*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]<br />
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==2016 (10)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
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*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]<br />
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*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]<br />
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*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]<br />
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*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
<br />
==2015 (14)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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 />}}]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
<br />
==2014 (5)-Sabbatical leave==<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 />
<br><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 />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
<br />
==2013 (2)==<br />
*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]<br />
<br><br />
*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]<br />
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<br />
==2012 (3)==<br />
*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] <br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
<br />
==2011 (5)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
<br />
==2010 (4)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
<br />
==2009 (3)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
==2008 (3)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<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><br />
==Before 2007 (12)==<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><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><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><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><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><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><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><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><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><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><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><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 />
<br></div>
Administrator
https://netbiolab.org/w/Publications
Publications
2021-07-15T13:19:07Z
<p>Administrator: </p>
<hr />
<div>*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]<br />
*[https://www.ibric.org/hanbitsa/treatise_index_for_author.php?Page=1&idauthorid=760 BRIC 한빛사논문]<br />
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]<br />
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]<br />
* '*' First authors; '**' Corresponding authors; <br />
==2021==<br />
*95. '''Jae-Won Cho*''', Hyo Sup Shim, Chang Young Lee, Seong Yong Park, Min Hee Hong, '''Insuk Lee**, Hye Ryun Kim**''' The importance of enhancer methylation for epigenetic regulation of tumorigenesis in squamous lung cancer. [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-9.zip Supplementary File]<br />
<br><br />
*94. '''Chan Yeong Kim*, Muyoung Lee*''', Sunmo Yang, Kyungnam Kim, Dongeun Yong, Hye Ryun Kim, '''Insuk Lee**''' Human reference gut microbiome comprising 5,414 prokaryotic species, including newly assembled genomes from under-represented Asian metagenomes [https://www.biorxiv.org/content/10.1101/2020.11.09.375873v1 '''''bioRxiv preprint'''''] <br />
<br><br />
*93. '''Jae-Won Cho*''', Jimin Son*, Sang-Jun Ha**, '''Insuk Lee**''', Systems biology analysis identifies TNFRSF9 as a functional marker of tumor-infiltrating regulatory T-cell enabling clinical outcome prediction in lung cancer '''''Computational and Structural Biotechnology Journal''''' 2021 Jan 21; 19:860-868 [https://pubmed.ncbi.nlm.nih.gov/33598101 pubmed] <br />
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*92. '''Tak Lee*''', '''Insuk Lee**''' Genome-wide Association Studies in Arabidopsis thaliana: Statistical Analysis and Network-Based Augmentation of Signals '''''Methods in Molecular Biology''''' 2020 Nov; 2200:187-210 [https://pubmed.ncbi.nlm.nih.gov/33175379 pubmed] [https://netbiolab.org/wiki/glucose_germrate.txt Supplementary File 1] [https://netbiolab.org/wiki/glucose_sig_accessions.txt Supplementary File 2]<br />
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==2020 (9)== <br />
*91. '''Junha Cha*''', '''Insuk Lee**''' Single-cell Network Biology for Resolving Cellular Heterogeneity in Human Diseases '''''Experimental & Molecular Medicine''''' 2020 Nov;52(11):1798-1808 [https://pubmed.ncbi.nlm.nih.gov/33244151 pubmed]<br />
<br><br />
*90. Jimin Son*, '''Jae-Won Cho*''', Hyo Jin Park, Jihyun Moon, Seyeon Park, Hoyoung Lee, Jeewon Lee, Ga min Kim, Su-Myeong Park, Sergio A. Lira, Andrew N. Mckenzie, Hye Young Kim, Cheol Yong Choi, Yong Taik Lim, Seong Yong Park, Hye Ryun Kim, Su-Hyung Park, Eui-Cheol Shin, '''Insuk Lee'''** & Sang-Jun Ha**, Tumor-Infiltrating Regulatory T Cell Accumulation in the Tumor Microenvironment is Mediated by IL33/ST2 Signaling '''''Cancer Immunology Research''''' 2020 Nov; 8(11):1393-1406 [https://pubmed.ncbi.nlm.nih.gov/32878747 pubmed] '''Spotlighted''' by [https://acir.org/journal-articles/cancer-immunobiology/immune-cell-biology?entryId=26357 Accelerating Cancer Immunotherapy Research]<br />
<br><br />
*89. '''Jae-Won Cho*''', Min Hee Hong, Sang-Jun Ha, Young-Joon Kim, Byoung Chul Cho, '''Insuk Lee**''', and Hye Ryun Kim** Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer [https://netbiolab.org/wiki/Supplementary_Table_S1-6.zip Supplementary File] '''''Experimental & Molecular Medicine''''' 2020 Sep 02;52(9):1550-1563 [https://pubmed.ncbi.nlm.nih.gov/32879421 pubmed]<br />
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*88. '''Seungbyn Baek*''', '''Insuk Lee**''' Single-cell ATAC sequencing analysis: from data preprocessing to hypothesis generation '''''Computational and Structural Biotechnology Journal''''' 2020 June 28;18:1429-1439 [https://pubmed.ncbi.nlm.nih.gov/32637041 pubmed]<br />
<br><br />
*87. '''Eiru Kim*, Dasom Bae*, Sunmo Yang*''', Gunhwan Ko, Sungho Lee, Byungwook Lee**, '''Insuk Lee**'''. BiomeNet: A database for construction and analysis of functional interaction networks for any species with a sequenced genome '''''Bioinformatics''''' 2020 Mar 1:36(5):1584-1589 [https://www.ncbi.nlm.nih.gov/pubmed/31599923 pubmed]<br />
<br><br />
*86. '''Kyungsoo Kim*''', Seyeon Park*, Seong Yong Park, Gamin Kim, Su Myeong Park, Jae-Won Cho, Da Hee Kim, Young Min Park, Yoon Woo Koh, Hye Ryun Kim, Sang-Jun Ha** and '''Insuk Lee**''', Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer '''''Genome Medicine''''' 2020 Feb 28;12:22 [https://pubmed.ncbi.nlm.nih.gov/32111241 pubmed]<br />
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*85. '''Sungho Lee*, Tak Lee*''', Sunmo Yang and '''Insuk Lee**''', BarleyNet: a network-based functional omics analysis server for cultivated barley, Hordeum vulgare L. '''''Frontiers in Plant Science''''' 2020 Feb 18;11:98 [https://pubmed.ncbi.nlm.nih.gov/32133024/ pubmed]<br />
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*84. '''Kyungsoo Kim*''', Sunmo Yang, Sang-Jun Ha, '''Insuk Lee**''', VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data '''''Bioinformatics''''' 2020 Jan 15;36(2):546-551 [https://www.ncbi.nlm.nih.gov/pubmed/31373613 pubmed]<br />
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*83. '''Jung Eun Shim*, Insuk Lee**''', Construction of functional protein networks using domain profile associations, '''''Methods in Molecular Biology''''' 2020 Jan;2074:35-44 [https://www.ncbi.nlm.nih.gov/pubmed/31583628 pubmed]<br />
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<br />
==2019 (6)== <br />
*82. '''Han H*''', Lee S, '''Lee I**''', NGSEA: network-based gene set enrichment analysis for interpreting gene expression phenotypes with functional gene sets '''''Mol Cells''''' 2019 Aug 31;42(8):579-588. [https://www.ncbi.nlm.nih.gov/pubmed/31307154 pubmed]<br />
<br><br />
*81. '''Lee T*, Lee S*''', Yang S, '''Lee I**'''. MaizeNet: A co-functional network for network-assisted systems genetics in Zea mays '''''The Plant Journal''''' 2019 Aug 99(3):571-582 [https://www.ncbi.nlm.nih.gov/pubmed/31006149 pubmed]<br />
<br><br />
*80. '''Lee M*''', Pinto NA*, Kim CY, Yang S, D'Souza R, Yong D**, Lee I**. Network integrative genomic and transcriptomic analysis of carbapenem-resistant Klebsiella pneumoniae strains identifies genes for antibiotic-resistance and virulence '''''mSystems''''' 2019 Aug;4(4):e00202-19. [https://www.ncbi.nlm.nih.gov/pubmed/31117026 pubmed] <br />
<br><br />
*79. '''Shim JE*''', Kim JH, Shin J, Lee JE, '''Lee I**''' Pathway-specific protein domains are predictive for human diseases '''''PLOS Computational Biology''''' 2019 May 10;15(5):e1007052 [https://www.ncbi.nlm.nih.gov/pubmed/31075101 pubmed] <br />
<br><br />
*78. '''Kim H*''', Joe A*, Lee M, Yang S, Ma X, Ronald PC**, '''Lee I**'''. A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems '''''Mol Cells''''' 2019 Feb 28;42(2):166-174 [https://www.ncbi.nlm.nih.gov/pubmed/30759970 pubmed]<br />
<br><br />
*77. '''Hwang S*, Kim CY*''', Yang S, Kim E, Hart T, Marcotte EM, '''Lee I**'''. HumanNet v2: human gene networks for disease research '''''Nucleic Acids Research''''' 2019 Jan 8;47(D1):D573–D580.[https://www.ncbi.nlm.nih.gov/pubmed/30418591 pubmed]<br />
<br><br />
<br />
==2018 (5)== <br />
*76. '''Han H*''', Lehner B, '''Lee I**''', Cancer gene discovery by network analysis of somatic mutations using the MUFFINN server, '''''Methods in Molecular Biology''''' 2018 Dec 13; 1907:37-50.[https://www.ncbi.nlm.nih.gov/pubmed/30542989 pubmed]<br />
<br><br />
*75. '''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. [https://www.ncbi.nlm.nih.gov/pubmed/30018396 pubmed]<br />
<br><br />
*74. Lim KT, Kim J, Hwang SI, Zhang L, Han H, Bae D, Kim KP, Hu YP, Schöler HR, '''Lee I''', Hui L, Han DW, Direct Conversion of Mouse Fibroblasts into Cholangiocyte Progenitor Cells. '''''Stem Cell Reports''''' 2018 Mar 27. 10:1-15.[https://www.ncbi.nlm.nih.gov/pubmed/29606616 pubmed]<br />
<br><br />
*73. '''Lee T*, Lee I**''', araGWAB: A web application for network-based boosting of genome-wide association signals in Arabidopsis '''''Scientific Reports''''' 2018 Feb 13;8(1):2925.[https://www.ncbi.nlm.nih.gov/pubmed/29440686 pubmed]<br />
<br><br />
*72. '''Han H*''', Cho JW, Lee S, Yun A, Kim H, Bae D, Yang S, Kim CY, Lee M, Kim E, Lee S, Kang B, Jeong D, Kim Y, Jeon HN, Jung H, Nam S, Chung M, Kim JH, '''Lee I**''', TRRUST v2: An expanded reference database of human and mouse transcriptional regulatory interactions '''''Nucleic Acids Research''''' 2018 Jan 4;46(D1):D380–D386.[https://www.ncbi.nlm.nih.gov/pubmed/29087512 pubmed]<br />
<br><br />
<br />
==2017 (10)== <br />
*71. '''Kim CY*, Lee I**''', Functional gene networks based on the gene neighborhood in metagenomes, '''''Animal Cells and Systems''''' 2017 Sept 29; 21:301-306; <br />
<br><br />
*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] <br />
<br><br />
*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]<br />
<br><br />
*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 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]<br />
<br><br />
*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 />}}]<br />
<br><br />
*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; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
<br />
==2016 (10)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
<br />
==2015 (14)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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 />}}]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
<br />
==2014 (5)-Sabbatical leave==<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 />
<br><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 />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
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<br />
==2013 (2)==<br />
*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]<br />
<br><br />
*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]<br />
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<br />
==2012 (3)==<br />
*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] <br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
<br />
==2011 (5)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
<br />
==2010 (4)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
<br />
==2009 (3)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
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==2008 (3)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<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 />
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==Before 2007 (12)==<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><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><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><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><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><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><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><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><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><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><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><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 />
<br></div>
Administrator
https://netbiolab.org/w/Publications
Publications
2021-07-15T11:52:56Z
<p>Administrator: </p>
<hr />
<div>*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]<br />
*[https://www.ibric.org/hanbitsa/treatise_index_for_author.php?Page=1&idauthorid=760 BRIC 한빛사논문]<br />
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]<br />
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]<br />
* '*' First authors; '**' Corresponding authors; <br />
==2021==<br />
*95. '''Jae-Won Cho*''', Hyo Sup Shim, Chang Young Lee, Seong Yong Park, Min Hee Hong, '''Insuk Lee**, Hye Ryun Kim**''' The importance of enhancer methylation for epigenetic regulation of tumorigenesis in squamous lung cancer. [//netbiolab.org/wiki/Supplementary_Table_S1-6.zip Supplementary File] <br />
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*94. '''Chan Yeong Kim*, Muyoung Lee*''', Sunmo Yang, Kyungnam Kim, Dongeun Yong, Hye Ryun Kim, '''Insuk Lee**''' Human reference gut microbiome comprising 5,414 prokaryotic species, including newly assembled genomes from under-represented Asian metagenomes [https://www.biorxiv.org/content/10.1101/2020.11.09.375873v1 '''''bioRxiv preprint'''''] <br />
<br><br />
*93. '''Jae-Won Cho*''', Jimin Son*, Sang-Jun Ha**, '''Insuk Lee**''', Systems biology analysis identifies TNFRSF9 as a functional marker of tumor-infiltrating regulatory T-cell enabling clinical outcome prediction in lung cancer '''''Computational and Structural Biotechnology Journal''''' 2021 Jan 21; 19:860-868 [https://pubmed.ncbi.nlm.nih.gov/33598101 pubmed] <br />
<br><br />
*92. '''Tak Lee*''', '''Insuk Lee**''' Genome-wide Association Studies in Arabidopsis thaliana: Statistical Analysis and Network-Based Augmentation of Signals '''''Methods in Molecular Biology''''' 2020 Nov; 2200:187-210 [https://pubmed.ncbi.nlm.nih.gov/33175379 pubmed] [https://netbiolab.org/wiki/glucose_germrate.txt Supplementary File 1] [https://netbiolab.org/wiki/glucose_sig_accessions.txt Supplementary File 2]<br />
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==2020 (9)== <br />
*91. '''Junha Cha*''', '''Insuk Lee**''' Single-cell Network Biology for Resolving Cellular Heterogeneity in Human Diseases '''''Experimental & Molecular Medicine''''' 2020 Nov;52(11):1798-1808 [https://pubmed.ncbi.nlm.nih.gov/33244151 pubmed]<br />
<br><br />
*90. Jimin Son*, '''Jae-Won Cho*''', Hyo Jin Park, Jihyun Moon, Seyeon Park, Hoyoung Lee, Jeewon Lee, Ga min Kim, Su-Myeong Park, Sergio A. Lira, Andrew N. Mckenzie, Hye Young Kim, Cheol Yong Choi, Yong Taik Lim, Seong Yong Park, Hye Ryun Kim, Su-Hyung Park, Eui-Cheol Shin, '''Insuk Lee'''** & Sang-Jun Ha**, Tumor-Infiltrating Regulatory T Cell Accumulation in the Tumor Microenvironment is Mediated by IL33/ST2 Signaling '''''Cancer Immunology Research''''' 2020 Nov; 8(11):1393-1406 [https://pubmed.ncbi.nlm.nih.gov/32878747 pubmed] '''Spotlighted''' by [https://acir.org/journal-articles/cancer-immunobiology/immune-cell-biology?entryId=26357 Accelerating Cancer Immunotherapy Research]<br />
<br><br />
*89. '''Jae-Won Cho*''', Min Hee Hong, Sang-Jun Ha, Young-Joon Kim, Byoung Chul Cho, '''Insuk Lee**''', and Hye Ryun Kim** Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer [https://netbiolab.org/wiki/Supplementary_Table_S1-6.zip Supplementary File] '''''Experimental & Molecular Medicine''''' 2020 Sep 02;52(9):1550-1563 [https://pubmed.ncbi.nlm.nih.gov/32879421 pubmed]<br />
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*88. '''Seungbyn Baek*''', '''Insuk Lee**''' Single-cell ATAC sequencing analysis: from data preprocessing to hypothesis generation '''''Computational and Structural Biotechnology Journal''''' 2020 June 28;18:1429-1439 [https://pubmed.ncbi.nlm.nih.gov/32637041 pubmed]<br />
<br><br />
*87. '''Eiru Kim*, Dasom Bae*, Sunmo Yang*''', Gunhwan Ko, Sungho Lee, Byungwook Lee**, '''Insuk Lee**'''. BiomeNet: A database for construction and analysis of functional interaction networks for any species with a sequenced genome '''''Bioinformatics''''' 2020 Mar 1:36(5):1584-1589 [https://www.ncbi.nlm.nih.gov/pubmed/31599923 pubmed]<br />
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*86. '''Kyungsoo Kim*''', Seyeon Park*, Seong Yong Park, Gamin Kim, Su Myeong Park, Jae-Won Cho, Da Hee Kim, Young Min Park, Yoon Woo Koh, Hye Ryun Kim, Sang-Jun Ha** and '''Insuk Lee**''', Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer '''''Genome Medicine''''' 2020 Feb 28;12:22 [https://pubmed.ncbi.nlm.nih.gov/32111241 pubmed]<br />
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*85. '''Sungho Lee*, Tak Lee*''', Sunmo Yang and '''Insuk Lee**''', BarleyNet: a network-based functional omics analysis server for cultivated barley, Hordeum vulgare L. '''''Frontiers in Plant Science''''' 2020 Feb 18;11:98 [https://pubmed.ncbi.nlm.nih.gov/32133024/ pubmed]<br />
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*84. '''Kyungsoo Kim*''', Sunmo Yang, Sang-Jun Ha, '''Insuk Lee**''', VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data '''''Bioinformatics''''' 2020 Jan 15;36(2):546-551 [https://www.ncbi.nlm.nih.gov/pubmed/31373613 pubmed]<br />
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*83. '''Jung Eun Shim*, Insuk Lee**''', Construction of functional protein networks using domain profile associations, '''''Methods in Molecular Biology''''' 2020 Jan;2074:35-44 [https://www.ncbi.nlm.nih.gov/pubmed/31583628 pubmed]<br />
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<br />
==2019 (6)== <br />
*82. '''Han H*''', Lee S, '''Lee I**''', NGSEA: network-based gene set enrichment analysis for interpreting gene expression phenotypes with functional gene sets '''''Mol Cells''''' 2019 Aug 31;42(8):579-588. [https://www.ncbi.nlm.nih.gov/pubmed/31307154 pubmed]<br />
<br><br />
*81. '''Lee T*, Lee S*''', Yang S, '''Lee I**'''. MaizeNet: A co-functional network for network-assisted systems genetics in Zea mays '''''The Plant Journal''''' 2019 Aug 99(3):571-582 [https://www.ncbi.nlm.nih.gov/pubmed/31006149 pubmed]<br />
<br><br />
*80. '''Lee M*''', Pinto NA*, Kim CY, Yang S, D'Souza R, Yong D**, Lee I**. Network integrative genomic and transcriptomic analysis of carbapenem-resistant Klebsiella pneumoniae strains identifies genes for antibiotic-resistance and virulence '''''mSystems''''' 2019 Aug;4(4):e00202-19. [https://www.ncbi.nlm.nih.gov/pubmed/31117026 pubmed] <br />
<br><br />
*79. '''Shim JE*''', Kim JH, Shin J, Lee JE, '''Lee I**''' Pathway-specific protein domains are predictive for human diseases '''''PLOS Computational Biology''''' 2019 May 10;15(5):e1007052 [https://www.ncbi.nlm.nih.gov/pubmed/31075101 pubmed] <br />
<br><br />
*78. '''Kim H*''', Joe A*, Lee M, Yang S, Ma X, Ronald PC**, '''Lee I**'''. A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems '''''Mol Cells''''' 2019 Feb 28;42(2):166-174 [https://www.ncbi.nlm.nih.gov/pubmed/30759970 pubmed]<br />
<br><br />
*77. '''Hwang S*, Kim CY*''', Yang S, Kim E, Hart T, Marcotte EM, '''Lee I**'''. HumanNet v2: human gene networks for disease research '''''Nucleic Acids Research''''' 2019 Jan 8;47(D1):D573–D580.[https://www.ncbi.nlm.nih.gov/pubmed/30418591 pubmed]<br />
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<br />
==2018 (5)== <br />
*76. '''Han H*''', Lehner B, '''Lee I**''', Cancer gene discovery by network analysis of somatic mutations using the MUFFINN server, '''''Methods in Molecular Biology''''' 2018 Dec 13; 1907:37-50.[https://www.ncbi.nlm.nih.gov/pubmed/30542989 pubmed]<br />
<br><br />
*75. '''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. [https://www.ncbi.nlm.nih.gov/pubmed/30018396 pubmed]<br />
<br><br />
*74. Lim KT, Kim J, Hwang SI, Zhang L, Han H, Bae D, Kim KP, Hu YP, Schöler HR, '''Lee I''', Hui L, Han DW, Direct Conversion of Mouse Fibroblasts into Cholangiocyte Progenitor Cells. '''''Stem Cell Reports''''' 2018 Mar 27. 10:1-15.[https://www.ncbi.nlm.nih.gov/pubmed/29606616 pubmed]<br />
<br><br />
*73. '''Lee T*, Lee I**''', araGWAB: A web application for network-based boosting of genome-wide association signals in Arabidopsis '''''Scientific Reports''''' 2018 Feb 13;8(1):2925.[https://www.ncbi.nlm.nih.gov/pubmed/29440686 pubmed]<br />
<br><br />
*72. '''Han H*''', Cho JW, Lee S, Yun A, Kim H, Bae D, Yang S, Kim CY, Lee M, Kim E, Lee S, Kang B, Jeong D, Kim Y, Jeon HN, Jung H, Nam S, Chung M, Kim JH, '''Lee I**''', TRRUST v2: An expanded reference database of human and mouse transcriptional regulatory interactions '''''Nucleic Acids Research''''' 2018 Jan 4;46(D1):D380–D386.[https://www.ncbi.nlm.nih.gov/pubmed/29087512 pubmed]<br />
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<br />
==2017 (10)== <br />
*71. '''Kim CY*, Lee I**''', Functional gene networks based on the gene neighborhood in metagenomes, '''''Animal Cells and Systems''''' 2017 Sept 29; 21:301-306; <br />
<br><br />
*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] <br />
<br><br />
*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]<br />
<br><br />
*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 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]<br />
<br><br />
*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 />}}]<br />
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*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; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
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*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]<br />
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*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]<br />
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<br />
==2016 (10)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
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<br />
==2015 (14)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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 />}}]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
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*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]<br />
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*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]<br />
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<br />
==2014 (5)-Sabbatical leave==<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 />
<br><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 />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
<br />
==2013 (2)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
<br />
==2012 (3)==<br />
*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] <br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
<br />
==2011 (5)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
<br />
==2010 (4)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
<br />
==2009 (3)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
==2008 (3)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<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><br />
==Before 2007 (12)==<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><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><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><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><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><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><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><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><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><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><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><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 />
<br></div>
Administrator
https://netbiolab.org/w/Welcome
Welcome
2021-02-26T19:42:23Z
<p>Administrator: </p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
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<div style="font-size:225%;font-weight:1000;">Welcome to Bioinformatics Laboratory</div><br />
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[[File:Web_main_2019.png|center|780px]]<br />
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=== Research Keyword Cloud (2018-2020)===<br />
<div>{{#widget:AddHtml|content=<img src="../wiki/wordcloud_2018_2020.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div><br />
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|-<br />
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=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| KS Kim<br />
|style="width:65px"| CY Kim<br />
|-<br />
|JW Cho<br />
|SH Lee<br />
|-<br />
|JH Cha<br />
|NY Kim<br />
|-<br />
|SB Baek<br />
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|}<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 />
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|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>
Administrator
https://netbiolab.org/w/Software
Software
2020-11-13T06:25:12Z
<p>Administrator: </p>
<hr />
<div>__NOTOC__<br />
[[File:Hrgm logo.png|200px|link=//www.mbiomenet.org/HRGM]]<br />
'''HRGM''': Human reference gut microbiome of 5,414 prokaryotic species including newly assembled genomes from under-represented Asian metagenomes.<br />
<br />
<br />
=='''Single-cell Omics Data Analysis Tools'''==<br />
[[File:VC_logo.png|200px|link=//www.grnpedia.org/cytometry]]<br />
'''VirtualCytometry''': A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.''<br />
<br />
<br />
=='''Network Medicine Tools '''==<br />
[[File:HumanNet_logo_with_title.png|150px|link=//www.inetbio.org/humannet]]'''HumanNet''': Human gene networks for disease research<br />
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<br />
[[File:TRRUST_logo.jpg |150px|link=//www.grnpedia.org/trrust/]] '''TRRUST''': Curated TF-target interaction networks in human and mouse<br />
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<br />
[[File:Ngsea logo1.png |150px|link=//www.inetbio.org/ngsea/]] '''NGSEA''': Network-augmented gene set enrichment analysis tool<br />
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<br />
[[File:Cover title muffinn.png |150px|link=//www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation data<br />
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<br />
[[File:GWAB_logo.png |150px|link=//www.inetbio.org/gwab]] '''GWAB''': A web server for network-based boosting of human genome-wide association data<br />
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<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=//www.inetbio.org/morphin/]] '''MORPHIN''': Network-assisted prediction of disease pathways in model organisms<br />
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<br />
[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only)<br />
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<br />
<br />
=='''Co-functional Gene Networks'''==<br />
<br />
==''Laboratory Animals''==<br />
{|border="0" width="400"<br />
|align="center"|[[file:MouseNetLogo.png|150px|link=//www.inetbio.org/mousenet]]<br />
|align="center"|[[file:danionet_logo.png|150px|link=//www.inetbio.org/danionet]]<br />
|align="center"|[[file:Flynet.png|150px|link=//www.inetbio.org/flynet]]<br />
|align="center"|[[file:WormNetv3.jpg|150px|link=//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=//www.inetbio.org/aranet]]<br />
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=//www.inetbio.org/maizenet]]<br />
|align="center"|[[file:RiceNetv2 logo.png|150px|link=//www.inetbio.org/ricenet]]<br />
|align="center"|[[File:WheatNet_logo.png|150px|link=//www.inetbio.org/wheatnet]]<br />
|align="center"|[[File:BarleyNet_logo.png|150px|link=//www.inetbio.org/barleynet]]<br />
|align="center"|[[File:Soynetlogo.png|150px|link=//www.inetbio.org/soynet]]<br />
|align="center"|[[File:Tomatonet_logo.png|150px|link=//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"|''Hordeum vulgare''<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=//www.inetbio.org/yeastnet]]<br />
|align="center"|[[file:CryptoNet.png|150px|link=//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=//www.inetbio.org/pseudomonasnet]]<br />
|align="center"|[[File:Staphnet_logo.JPG|150px|link=//www.inetbio.org/staphnet]]<br />
|align="center"|[[File:KlebNet_logo.png|150px|link=//www.inetbio.org/klebnet]]<br />
|align="center"|[[File:EcoliNet.png|150px|link=//www.inetbio.org/ecolinet]]<br />
|align="center"|[[File:XooNet_logo.png|150px|link=//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 />
<br />
==''Build your own co-functional networks''==<br />
[[File:BiomeNet_logo.png | 150px | link=http://kobic.re.kr/biomenet]]<br />
'''BiomeNet''': A database for construction and analysis of functional interaction networks for any species with a sequenced genome<br />
<br />
<br />
<br />
=='''Network-augmented GWAS Analysis for Arabidopsis'''==<br />
[[File:araGWAB_logo.png|150px|link=//www.inetbio.org/aragwab]]<br />
'''araGWAB''': genome-wide association boosting for ''Arabidopsis thaliana''<br />
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<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>
Administrator
https://netbiolab.org/w/File:Hrgm_logo.png
File:Hrgm logo.png
2020-11-13T06:20:26Z
<p>Administrator: </p>
<hr />
<div></div>
Administrator
https://netbiolab.org/w/Publications
Publications
2020-09-18T13:13:43Z
<p>Administrator: </p>
<hr />
<div>*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]<br />
*[https://www.ibric.org/hanbitsa/treatise_index_for_author.php?Page=1&idauthorid=760 BRIC 한빛사논문]<br />
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]<br />
* '*' First authors; '**' Corresponding authors; <br />
==2021== <br />
<br />
==2020 (10)== <br />
*92. '''Tak Lee*''', '''Insuk Lee**''' Genome-wide Association Studies in Arabidopsis thaliana: Statistical Analysis and Network-Based Augmentation of Signals '''''Arabidopsis Protocols 4th Ed.''''' [https://netbiolab.org/wiki/glucose_germrate.txt Supplementary File 1] [https://netbiolab.org/wiki/glucose_sig_accessions.txt Supplementary File 2] In press<br />
<br><br />
*91. '''Junha Cha*''', '''Insuk Lee**''' Single-cell Network Biology for Resolving Cellular Heterogeneity in Human Diseases '''''Experimental & Molecular Medicine''''' accepted <br />
<br><br />
*90. Jimin Son*, '''Jae-Won Cho*''', Hyo Jin Park, Jihyun Moon, Seyeon Park, Hoyoung Lee, Jeewon Lee, Ga min Kim, Su-Myeong Park, Sergio A. Lira, Andrew N. Mckenzie, Hye Young Kim, Cheol Yong Choi, Yong Taik Lim, Seong Yong Park, Hye Ryun Kim, Su-Hyung Park, Eui-Cheol Shin, '''Insuk Lee'''** & Sang-Jun Ha**, Tumor-Infiltrating Regulatory T Cell Accumulation in the Tumor Microenvironment is Mediated by IL33/ST2 Signaling '''''Cancer Immunology Research''''' [https://pubmed.ncbi.nlm.nih.gov/32878747 pubmed]<br />
<br><br />
*89. '''Jae-Won Cho*''', Min Hee Hong, Sang-Jun Ha, Young-Joon Kim, Byoung Chul Cho, '''Insuk Lee**''', and Hye Ryun Kim** Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer [https://netbiolab.org/wiki/Supplementary_Table_S1-6.zip Supplementary File] '''''Experimental & Molecular Medicine''''' [https://pubmed.ncbi.nlm.nih.gov/32879421 pubmed]<br />
<br><br />
*88. '''Seungbyn Baek*''', '''Insuk Lee**''' Single-cell ATAC sequencing analysis: from data preprocessing to hypothesis generation '''''Computational and Structural Biotechnology Journal''''' 2020 June 28;18:1429-1439 [https://pubmed.ncbi.nlm.nih.gov/32637041 pubmed]<br />
<br><br />
*87. '''Eiru Kim*, Dasom Bae*, Sunmo Yang*''', Gunhwan Ko, Sungho Lee, Byungwook Lee**, '''Insuk Lee**'''. BiomeNet: A database for construction and analysis of functional interaction networks for any species with a sequenced genome '''''Bioinformatics''''' 2020 Mar 1:36(5):1584-1589 [https://www.ncbi.nlm.nih.gov/pubmed/31599923 pubmed]<br />
<br><br />
*86. '''Kyungsoo Kim*''', Seyeon Park*, Seong Yong Park, Gamin Kim, Su Myeong Park, Jae-Won Cho, Da Hee Kim, Young Min Park, Yoon Woo Koh, Hye Ryun Kim, Sang-Jun Ha** and '''Insuk Lee**''', Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer '''''Genome Medicine''''' 2020 Feb 28;12:22 [https://pubmed.ncbi.nlm.nih.gov/32111241 pubmed]<br />
<br><br />
*85. '''Sungho Lee*, Tak Lee*''', Sunmo Yang and '''Insuk Lee**''', BarleyNet: a network-based functional omics analysis server for cultivated barley, Hordeum vulgare L. '''''Frontiers in Plant Science''''' 2020 Feb 18;11:98 [https://pubmed.ncbi.nlm.nih.gov/32133024/ pubmed]<br />
<br><br />
*84. '''Kyungsoo Kim*''', Sunmo Yang, Sang-Jun Ha, '''Insuk Lee**''', VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data '''''Bioinformatics''''' 2020 Jan 15;36(2):546-551 [https://www.ncbi.nlm.nih.gov/pubmed/31373613 pubmed]<br />
<br><br />
*83. '''Jung Eun Shim*, Insuk Lee**''', Construction of functional protein networks using domain profile associations, '''''Methods in Molecular Biology''''' 2020 Jan;2074:35-44 [https://www.ncbi.nlm.nih.gov/pubmed/31583628 pubmed]<br />
<br><br />
<br />
==2019 (6)== <br />
*82. '''Han H*''', Lee S, '''Lee I**''', NGSEA: network-based gene set enrichment analysis for interpreting gene expression phenotypes with functional gene sets '''''Mol Cells''''' 2019 Aug 31;42(8):579-588. [https://www.ncbi.nlm.nih.gov/pubmed/31307154 pubmed]<br />
<br><br />
*81. '''Lee T*, Lee S*''', Yang S, '''Lee I**'''. MaizeNet: A co-functional network for network-assisted systems genetics in Zea mays '''''The Plant Journal''''' 2019 Aug 99(3):571-582 [https://www.ncbi.nlm.nih.gov/pubmed/31006149 pubmed]<br />
<br><br />
*80. '''Lee M*''', Pinto NA*, Kim CY, Yang S, D'Souza R, Yong D**, Lee I**. Network integrative genomic and transcriptomic analysis of carbapenem-resistant Klebsiella pneumoniae strains identifies genes for antibiotic-resistance and virulence '''''mSystems''''' 2019 Aug;4(4):e00202-19. [https://www.ncbi.nlm.nih.gov/pubmed/31117026 pubmed] <br />
<br><br />
*79. '''Shim JE*''', Kim JH, Shin J, Lee JE, '''Lee I**''' Pathway-specific protein domains are predictive for human diseases '''''PLOS Computational Biology''''' 2019 May 10;15(5):e1007052 [https://www.ncbi.nlm.nih.gov/pubmed/31075101 pubmed] <br />
<br><br />
*78. '''Kim H*''', Joe A*, Lee M, Yang S, Ma X, Ronald PC**, '''Lee I**'''. A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems '''''Mol Cells''''' 2019 Feb 28;42(2):166-174 [https://www.ncbi.nlm.nih.gov/pubmed/30759970 pubmed]<br />
<br><br />
*77. '''Hwang S*, Kim CY*''', Yang S, Kim E, Hart T, Marcotte EM, '''Lee I**'''. HumanNet v2: human gene networks for disease research '''''Nucleic Acids Research''''' 2019 Jan 8;47(D1):D573–D580.[https://www.ncbi.nlm.nih.gov/pubmed/30418591 pubmed]<br />
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<br />
==2018 (5)== <br />
*76. '''Han H*''', Lehner B, '''Lee I**''', Cancer gene discovery by network analysis of somatic mutations using the MUFFINN server, '''''Methods in Molecular Biology''''' 2018 Dec 13; 1907:37-50.[https://www.ncbi.nlm.nih.gov/pubmed/30542989 pubmed]<br />
<br><br />
*75. '''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. [https://www.ncbi.nlm.nih.gov/pubmed/30018396 pubmed]<br />
<br><br />
*74. Lim KT, Kim J, Hwang SI, Zhang L, Han H, Bae D, Kim KP, Hu YP, Schöler HR, '''Lee I''', Hui L, Han DW, Direct Conversion of Mouse Fibroblasts into Cholangiocyte Progenitor Cells. '''''Stem Cell Reports''''' 2018 Mar 27. 10:1-15.[https://www.ncbi.nlm.nih.gov/pubmed/29606616 pubmed]<br />
<br><br />
*73. '''Lee T*, Lee I**''', araGWAB: A web application for network-based boosting of genome-wide association signals in Arabidopsis '''''Scientific Reports''''' 2018 Feb 13;8(1):2925.[https://www.ncbi.nlm.nih.gov/pubmed/29440686 pubmed]<br />
<br><br />
*72. '''Han H*''', Cho JW, Lee S, Yun A, Kim H, Bae D, Yang S, Kim CY, Lee M, Kim E, Lee S, Kang B, Jeong D, Kim Y, Jeon HN, Jung H, Nam S, Chung M, Kim JH, '''Lee I**''', TRRUST v2: An expanded reference database of human and mouse transcriptional regulatory interactions '''''Nucleic Acids Research''''' 2018 Jan 4;46(D1):D380–D386.[https://www.ncbi.nlm.nih.gov/pubmed/29087512 pubmed]<br />
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<br />
==2017 (10)== <br />
*71. '''Kim CY*, Lee I**''', Functional gene networks based on the gene neighborhood in metagenomes, '''''Animal Cells and Systems''''' 2017 Sept 29; 21:301-306; <br />
<br><br />
*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] <br />
<br><br />
*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]<br />
<br><br />
*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 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]<br />
<br><br />
*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 />}}]<br />
<br><br />
*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; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
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<br />
==2016 (10)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
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*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]<br />
<br><br />
*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]<br />
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<br />
==2015 (14)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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 />}}]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
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<br />
==2014 (5)-Sabbatical leave==<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 />
<br><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 />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
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<br />
==2013 (2)==<br />
*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]<br />
<br><br />
*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]<br />
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<br />
==2012 (3)==<br />
*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] <br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
<br />
==2011 (5)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
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*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]]<br />
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<br />
==2010 (4)==<br />
*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]]<br />
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*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]]<br />
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*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]]<br />
<br><br />
*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]]<br />
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<br />
==2009 (3)==<br />
*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]]<br />
<br><br />
*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]]<br />
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*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]]<br />
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==2008 (3)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<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 />
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==Before 2007 (12)==<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><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><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><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><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><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><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><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><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><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><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><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 />
<br></div>
Administrator
https://netbiolab.org/w/Publications
Publications
2020-06-17T10:54:31Z
<p>Administrator: </p>
<hr />
<div>*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]<br />
*[https://www.ibric.org/hanbitsa/treatise_index_for_author.php?Page=1&idauthorid=760 BRIC 한빛사논문]<br />
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]<br />
* '*' First authors; '**' Corresponding authors; <br />
==2020== <br />
*90. '''Jae-Won Cho*''', Min Hee Hong, Sang-Jun Ha, Young-Joon Kim, Byoung Chul Cho, '''Insuk Lee**''', and '''Hye Ryun Kim**''' Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer [https://netbiolab.org/wiki/Supplementary_Table_S1-6.zip Supplementary File] '''''Under review'''''<br />
<br><br />
*89. '''Tak Lee*''', '''Insuk Lee**''' Genome-wide Association Studies in Arabidopsis thaliana: Statistical Analysis and Network-Based Augmentation of Signals '''''Arabidopsis Protocols 4th Ed.''''' [https://netbiolab.org/wiki/glucose_germrate.txt Supplementary File] In press<br />
<br><br />
*88. '''Seungbyn Baek*''', '''Insuk Lee**''' Single-cell ATAC sequencing analysis: from data preprocessing to hypothesis generation '''''Computational and Structural Biotechnology Journal''''' 2020 In press <br />
<br><br />
*87. '''Eiru Kim*, Dasom Bae*, Sunmo Yang*''', Gunhwan Ko, Sungho Lee, '''Byungwook Lee**, Insuk Lee**'''. BiomeNet: A database for construction and analysis of functional interaction networks for any species with a sequenced genome '''''Bioinformatics''''' 2020 Mar 1:36(5):1584-1589 [https://www.ncbi.nlm.nih.gov/pubmed/31599923 pubmed]<br />
<br><br />
*86. '''Kyungsoo Kim*''', Seyeon Park*, Seong Yong Park, Gamin Kim, Su Myeong Park, Jae-Won Cho, Da Hee Kim, Young Min Park, Yoon Woo Koh, Hye Ryun Kim, Sang-Jun Ha** and '''Insuk Lee**''', Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer '''''Genome Medicine''''' 2020 Feb 28;12:22 [https://pubmed.ncbi.nlm.nih.gov/32111241 pubmed]<br />
<br><br />
*85. '''Sungho Lee*, Tak Lee*''', Sunmo Yang and '''Insuk Lee**''', BarleyNet: a network-based functional omics analysis server for cultivated barley, Hordeum vulgare L. '''''Frontiers in Plant Science''''' 2020 Feb 18;11:98 [https://pubmed.ncbi.nlm.nih.gov/32133024/ pubmed]<br />
<br><br />
*84. '''Kyungsoo Kim*''', Sunmo Yang, Sang-Jun Ha, '''Insuk Lee**''', VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data '''''Bioinformatics''''' 2020 Jan 15;36(2):546-551 [https://www.ncbi.nlm.nih.gov/pubmed/31373613 pubmed]<br />
<br><br />
*83. '''Jung Eun Shim*, Insuk Lee**''', Construction of functional protein networks using domain profile associations, '''''Methods in Molecular Biology''''' 2020 Jan;2074:35-44 [https://www.ncbi.nlm.nih.gov/pubmed/31583628 pubmed]<br />
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<br />
==2019 (6)== <br />
*82. '''Han H*''', Lee S, '''Lee I**''', NGSEA: network-based gene set enrichment analysis for interpreting gene expression phenotypes with functional gene sets '''''Mol Cells''''' 2019 Aug 31;42(8):579-588. [https://www.ncbi.nlm.nih.gov/pubmed/31307154 pubmed]<br />
<br><br />
*81. '''Lee T*, Lee S*''', Yang S, '''Lee I**'''. MaizeNet: A co-functional network for network-assisted systems genetics in Zea mays '''''The Plant Journal''''' 2019 Aug 99(3):571-582 [https://www.ncbi.nlm.nih.gov/pubmed/31006149 pubmed]<br />
<br><br />
*80. '''Lee M*''', Pinto NA*, Kim CY, Yang S, D'Souza R, Yong D**, Lee I**. Network integrative genomic and transcriptomic analysis of carbapenem-resistant Klebsiella pneumoniae strains identifies genes for antibiotic-resistance and virulence '''''mSystems''''' 2019 Aug;4(4):e00202-19. [https://www.ncbi.nlm.nih.gov/pubmed/31117026 pubmed] <br />
<br><br />
*79. '''Shim JE*''', Kim JH, Shin J, Lee JE, '''Lee I**''' Pathway-specific protein domains are predictive for human diseases '''''PLOS Computational Biology''''' 2019 May 10;15(5):e1007052 [https://www.ncbi.nlm.nih.gov/pubmed/31075101 pubmed] <br />
<br><br />
*78. '''Kim H*''', Joe A*, Lee M, Yang S, Ma X, Ronald PC**, '''Lee I**'''. A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems '''''Mol Cells''''' 2019 Feb 28;42(2):166-174 [https://www.ncbi.nlm.nih.gov/pubmed/30759970 pubmed]<br />
<br><br />
*77. '''Hwang S*, Kim CY*''', Yang S, Kim E, Hart T, Marcotte EM, '''Lee I**'''. HumanNet v2: human gene networks for disease research '''''Nucleic Acids Research''''' 2019 Jan 8;47(D1):D573–D580.[https://www.ncbi.nlm.nih.gov/pubmed/30418591 pubmed]<br />
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<br />
==2018 (5)== <br />
*76. '''Han H*''', Lehner B, '''Lee I**''', Cancer gene discovery by network analysis of somatic mutations using the MUFFINN server, '''''Methods in Molecular Biology''''' 2018 Dec 13; 1907:37-50.[https://www.ncbi.nlm.nih.gov/pubmed/30542989 pubmed]<br />
<br><br />
*75. '''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. [https://www.ncbi.nlm.nih.gov/pubmed/30018396 pubmed]<br />
<br><br />
*74. Lim KT, Kim J, Hwang SI, Zhang L, Han H, Bae D, Kim KP, Hu YP, Schöler HR, '''Lee I''', Hui L, Han DW, Direct Conversion of Mouse Fibroblasts into Cholangiocyte Progenitor Cells. '''''Stem Cell Reports''''' 2018 Mar 27. 10:1-15.[https://www.ncbi.nlm.nih.gov/pubmed/29606616 pubmed]<br />
<br><br />
*73. '''Lee T*, Lee I**''', araGWAB: A web application for network-based boosting of genome-wide association signals in Arabidopsis '''''Scientific Reports''''' 2018 Feb 13;8(1):2925.[https://www.ncbi.nlm.nih.gov/pubmed/29440686 pubmed]<br />
<br><br />
*72. '''Han H*''', Cho JW, Lee S, Yun A, Kim H, Bae D, Yang S, Kim CY, Lee M, Kim E, Lee S, Kang B, Jeong D, Kim Y, Jeon HN, Jung H, Nam S, Chung M, Kim JH, '''Lee I**''', TRRUST v2: An expanded reference database of human and mouse transcriptional regulatory interactions '''''Nucleic Acids Research''''' 2018 Jan 4;46(D1):D380–D386.[https://www.ncbi.nlm.nih.gov/pubmed/29087512 pubmed]<br />
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<br />
==2017 (10)== <br />
*71. '''Kim CY*, Lee I**''', Functional gene networks based on the gene neighborhood in metagenomes, '''''Animal Cells and Systems''''' 2017 Sept 29; 21:301-306; <br />
<br><br />
*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] <br />
<br><br />
*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]<br />
<br><br />
*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 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]<br />
<br><br />
*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 />}}]<br />
<br><br />
*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; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
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*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]<br />
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*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]<br />
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<br />
==2016 (10)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
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<br />
==2015 (14)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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 />}}]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
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*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]<br />
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*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]<br />
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<br />
==2014 (5)-Sabbatical leave==<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 />
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*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 />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
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<br />
==2013 (2)==<br />
*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]<br />
<br><br />
*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]<br />
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<br />
==2012 (3)==<br />
*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] <br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
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<br />
==2011 (5)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
<br />
==2010 (4)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
<br />
==2009 (3)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
==2008 (3)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<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><br />
==Before 2007 (12)==<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><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><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><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><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><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><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><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><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><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><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><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 />
<br></div>
Administrator
https://netbiolab.org/w/Welcome
Welcome
2020-06-01T01:54:57Z
<p>Administrator: </p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
|colspan="3"|<br />
<div style="font-size:225%;font-weight:1000;">Welcome to Bioinformatics Laboratory</div><br />
<br />
|-<br />
|rowspan="2" style="padding-right:20px;"|<br />
[[File:Web_main_2019.png|center|780px]]<br />
<br />
|colspan=2|<br />
<br />
=== Research Keyword Cloud (2013-2017)===<br />
<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><br />
<br />
|-<br />
|<br />
=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| KS Kim<br />
|style="width:65px"| CY Kim<br />
|-<br />
|JW Cho<br />
|SH Lee<br />
|-<br />
|JH Cha<br />
|NY Kim<br />
|-<br />
|SB Baek<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>
Administrator
https://netbiolab.org/w/Welcome
Welcome
2020-06-01T01:45:56Z
<p>Administrator: </p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
|colspan="3"|<br />
<div style="font-size:225%;font-weight:1000;">Welcome to Network Bioinformatics Laboratory</div><br />
<br />
|-<br />
|rowspan="2" style="padding-right:20px;"|<br />
[[File:Web_main_2019.png|center|780px]]<br />
<br />
|colspan=2|<br />
<br />
=== Research Keyword Cloud (2013-2017)===<br />
<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><br />
<br />
|-<br />
|<br />
=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| KS Kim<br />
|style="width:65px"| CY Kim<br />
|-<br />
|JW Cho<br />
|SH Lee<br />
|-<br />
|JH Cha<br />
|NY Kim<br />
|-<br />
|SB Baek<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>
Administrator
https://netbiolab.org/w/Software
Software
2019-10-17T05:53:20Z
<p>Administrator: </p>
<hr />
<div>__NOTOC__<br />
=='''Single-cell Omics Data Analysis Tools'''==<br />
[[File:VC_logo.png|200px|link=//www.grnpedia.org/cytometry]]<br />
'''VirtualCytometry''': A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.''<br />
<br />
<br />
=='''Network Medicine Tools '''==<br />
[[File:HumanNet_logo_with_title.png|150px|link=//www.inetbio.org/humannet]]'''HumanNet''': Human gene networks for disease research<br />
<br />
<br />
[[File:TRRUST_logo.jpg |150px|link=//www.grnpedia.org/trrust/]] '''TRRUST''': Curated TF-target interaction networks in human and mouse<br />
<br />
<br />
[[File:Ngsea logo1.png |150px|link=//www.inetbio.org/ngsea/]] '''NGSEA''': Network-augmented gene set enrichment analysis tool<br />
<br />
<br />
[[File:Cover title muffinn.png |150px|link=//www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation data<br />
<br />
<br />
[[File:GWAB_logo.png |150px|link=//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=//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 />
<br />
<br />
=='''Co-functional Gene Networks'''==<br />
<br />
==''Laboratory Animals''==<br />
{|border="0" width="400"<br />
|align="center"|[[file:MouseNetLogo.png|150px|link=//www.inetbio.org/mousenet]]<br />
|align="center"|[[file:danionet_logo.png|150px|link=//www.inetbio.org/danionet]]<br />
|align="center"|[[file:Flynet.png|150px|link=//www.inetbio.org/flynet]]<br />
|align="center"|[[file:WormNetv3.jpg|150px|link=//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=//www.inetbio.org/aranet]]<br />
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=//www.inetbio.org/maizenet]]<br />
|align="center"|[[file:RiceNetv2 logo.png|150px|link=//www.inetbio.org/ricenet]]<br />
|align="center"|[[File:WheatNet_logo.png|150px|link=//www.inetbio.org/wheatnet]]<br />
|align="center"|[[File:BarleyNet_logo.png|150px|link=//www.inetbio.org/barleynet]]<br />
|align="center"|[[File:Soynetlogo.png|150px|link=//www.inetbio.org/soynet]]<br />
|align="center"|[[File:Tomatonet_logo.png|150px|link=//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"|''Hordeum vulgare''<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=//www.inetbio.org/yeastnet]]<br />
|align="center"|[[file:CryptoNet.png|150px|link=//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=//www.inetbio.org/pseudomonasnet]]<br />
|align="center"|[[File:Staphnet_logo.JPG|150px|link=//www.inetbio.org/staphnet]]<br />
|align="center"|[[File:KlebNet_logo.png|150px|link=//www.inetbio.org/klebnet]]<br />
|align="center"|[[File:EcoliNet.png|150px|link=//www.inetbio.org/ecolinet]]<br />
|align="center"|[[File:XooNet_logo.png|150px|link=//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 />
<br />
==''Build your own co-functional networks''==<br />
[[File:BiomeNet_logo.png | 150px | link=http://kobic.re.kr/biomenet]]<br />
'''BiomeNet''': A database for construction and analysis of functional interaction networks for any species with a sequenced genome<br />
<br />
<br />
<br />
=='''Network-augmented GWAS Analysis for Arabidopsis'''==<br />
[[File:araGWAB_logo.png|150px|link=//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>
Administrator
https://netbiolab.org/w/File:BarleyNet_logo.png
File:BarleyNet logo.png
2019-10-17T05:46:35Z
<p>Administrator: </p>
<hr />
<div></div>
Administrator
https://netbiolab.org/w/Software
Software
2019-10-14T02:07:39Z
<p>Administrator: /* Build your own co-functional networks */</p>
<hr />
<div>__NOTOC__<br />
=='''Single-cell Omics Data Analysis Tools'''==<br />
[[File:VC_logo.png|200px|link=http://www.grnpedia.org/cytometry]]<br />
'''VirtualCytometry''': A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.''<br />
<br />
<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:Ngsea logo1.png |150px|link=https://www.inetbio.org/ngsea/]] '''NGSEA''': Network-augmented gene set enrichment analysis tool<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 />
<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:BiomeNet_logo.png | 150px | link=http://kobic.re.kr/biomenet]]<br />
'''BiomeNet''': A database for construction and analysis of functional interaction networks for any species with a sequenced genome<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>
Administrator
https://netbiolab.org/w/File:BiomeNet_logo.png
File:BiomeNet logo.png
2019-10-14T02:05:24Z
<p>Administrator: </p>
<hr />
<div></div>
Administrator
https://netbiolab.org/w/People
People
2019-08-23T02:20:30Z
<p>Administrator: </p>
<hr />
<div>__NOTOC__<br />
=='''Principal Investigator'''==<br />
{|border="0" width="150"<br />
|align="center"|[[File:이인석-2011사진.jpg|90px|link=people:IS_Lee]]<br />
|-<br />
|align="center"|[[people:IS_Lee|<big>'''Insuk Lee'''</big>]]<br />
|-<br />
|}<br />
<br />
=='''Research Staff'''==<br />
{|border="0" width="400"<br />
|align="center"|[[File:Smyang.jpg|70px|link=people:SM_Yang]]<br />
|align="center"|[[File:SYLee.jpg|70px|link=people:SY_Lee]]<br />
|align="center"|[[File:MYLee.png|70px|link=people:MY_Lee]]<br />
|-<br />
|align="center"|[[people:SM_Yang|<big>'''Sunmo Yang'''</big>]]<br />
|align="center"|[[people:SY_Lee|<big>'''Sangyoung Lee'''</big>]]<br />
|align="center"|[[people:MY_Lee|<big>'''Muyoung Lee'''</big>]]<br />
|-<br />
|align="center"|[[people:SM_Yang|Bioinformatics<br/>Programmer<br/>& Sys. Admin]]<br />
|align="center"|[[people:SY_Lee|Senior<br/>Research Assistant]]<br />
|align="center"|[[people:MY_Lee|Research Staff]]<br />
|}<br />
<br />
=='''Graduate Students'''==<br />
{|border="0" width="800"<br />
<br />
|align="center" |[[File:People_KSKim.jpg|70px|link=people:KS_Kim]]<br />
|align="center"|[[File:cykim.PNG|70px|link=People:CY_Kim]]<br />
|align="center"|[[File:Cho_JW.png|70px|link=People:J_Cho]]<br />
|align="center"|[[File:Shlee profile.png|70px|link=People:S_Lee]]<br />
|align="center"|[[File:Who.png|70px|link=People:JH_Cha]]<br />
|align="center"|[[File:Who.png|70px|link=People:NY_Kim]]<br />
|align="center"|[[File:Who.png|70px|link=People:SB_Baek]]<br />
|-<br />
<br />
|align="center"|[[people:KS_Kim|<big>'''Kyungsoo Kim'''</big>]]<br />
|align="center"|[[People:CY Kim|<big>'''Chan Yeong Kim'''</big>]]<br />
|align="center"|[[People:J_Cho|<big>'''Jae Won Cho'''</big>]]<br />
|align="center"|[[People:S_Lee|<big>'''Sungho Lee'''</big>]]<br />
|align="center"|[[People:JH_Cha|<big>'''Junha Cha'''</big>]]<br />
|align="center"|[[People:NY_Kim|<big>'''Nayeon Kim'''</big>]]<br />
|align="center"|[[People:SB_Baek|<big>'''Seungbyn Baek'''</big>]]<br />
|-<br />
<br />
|align="center"|[[people:KS_Kim|PhD candidate<br/>(2013.3 - )]]<br />
|align="center"|[[people:CY Kim|PhD candidate<br/>(2015.3 - )]]<br />
|align="center"|[[people:J_Cho|PhD candidate<br/>(2016.9 - )]]<br />
|align="center"|[[People:S_Lee|PhD course<br/>(2017.3 - )]]<br />
|align="center"|[[People:S_Lee|Master's course<br/>(2019.9 - )]]<br />
|align="center"|[[People:S_Lee|Master's course<br/>(2019.9 - )]]<br />
|align="center"|[[People:S_Lee|Master's course<br/>(2019.9 - )]]<br />
|}<br />
<br />
=='''Undergraduate Students'''==<br />
*Il Seok Choi<br />
<br />
=='''Alumni'''==<br />
*'''Former Post-docs and Staff Scientists'''<br />
**Taeyun Oh (2009.5-2011.12), currently Deputy Principal Consultant (인실리코젠 생명정보분석컨설턴트), [http://www.insilicogen.com INSILICOGEN], Korea <br />
**Sohyun Hwang (2010.3-2015.8), currently Assistant Professor (차의과대학 의과학과 교수), [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, The Mount Desert Island Biological Laboratory, Maine, USA (미국 MDI 생명과학연구소 교수), [https://mdibl.org/faculty/sam-beck-ph-d/ Lab Homepage]<br />
**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<br />
**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 <br />
**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 <br />
**Jung Eun Shim (2009.8-2017.11), currently Researcher at Yonsei Genomics Center Bioinformatics Data Analysis Core (연세의료원 유전체센터 생명정보분석코어 선임연구원)<br />
<br />
*'''Former Graduate Students (PhD)'''<br />
**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]<br />
**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)]<br />
**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)]<br />
**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]<br />
**Tak Lee (2011.3-2017.2), PhD; currently Postdoc Fellow, Sainsbury Laboratory at University of Cambridge, UK (영국 케임브리지대학 박사후연구원) [https://www.slcu.cam.ac.uk/research/oldroyd-group Oldroyd Lab] [https://www.slcu.cam.ac.uk/research/ahnert-group Ahnert Lab]<br />
**Heonjong Han (2011.1~2019.8), PhD; currently Postdoc Fellow, National Cancer Center, Korea (국립암센터 박사후연구원) [https://www.ncc.re.kr/ NCC]<br />
<br />
*'''Former Graduate Students (Master)'''<br />
**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<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<br />
**Muyoung Lee (2016.3-2018.2), M.Eng. currently Research staff, Yonsei University<br />
<br />
*'''Former Visiting Scientists/Students'''<br />
**Minkyung Shin (2012.3-2012.7), went to University of Southern California graduate school<br />
**Paul Chung (2012 summer), currently E-Commerce Analyst/Coordinator at [http://www.riotgames.com/ Riot Games], USA<br />
**Susie Shin (2013 summer)<br />
**Hyunjin Cho (2014 summer), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA<br />
**Michael Chung (2016.8-2016.12), currently work at [https://www.facebook.com/ Facebook], USA<br />
<br />
*'''Former Undergraduate Students'''<br />
**Ila Shin, went to medical school (Yonsei Univ.)<br />
**Yoonkyung Ko<br />
**Sangyo Park, went to law school (Kyounghee Univ.)<br />
**Jayoon Shin, went to medical school (Pusan National Univ.)<br />
**Dongjoo Sun, went to dental school (Wongwang Univ.)<br />
**Eulsoo Kim<br />
**Myungwhan Lee, went to medical school (Yonsei Univ.)<br />
**Moonhee Lee, went to graduate school (University of Amsterdam, Netherlands)<br />
**Jinhyun Ju, went to graduate school (Cornell Medical School, Computational Systems Biology); Currently Bioinformatics Scientist, Illumina, San Diego, USA (현재 미국 Illumina 본사 근무) <br />
**Haeyoung Shin, went to graduate school (Brown University, Computational Neuroscience)<br />
**Joonghee Soh, went to graduate school (KAIST, Culture Technology)<br />
**Hee Jung Cho, went to graduate school (UC Berkeley) <br />
**TaeHwan Kim, went to medical school<br />
**Joohyung Kim, went to medical school (Kyungpook National Univ.)<br />
**Donghyun Shin, went to medical school (Yonsei Univ.)<br />
**Byunghee Kang (2015 spring - 2016 summer), went to graduate school (PosTech)<br />
**Sunphil Kim (2016 winter)<br />
**Jaeho Shim (2016 winter)<br />
**Seunghyun Shin (2016 spring)<br />
**Aejoo Hong (2016 spring)<br />
**Changbae Bang (2016 summer), went to medical school (Yonsei Univ.)<br />
**Seoyoung Choi (2016 summer)<br />
**Dabin Jung (2016 summer)<br />
**Boreum Nam (2016 summer)<br />
**Seungun Lee (2016 summer)<br />
**Yeaji Kim (2016 summer and fall)<br />
**Sangyoung Lee (2017 winter)<br />
**Heejun Jang (2017 winter & spring), went to KIST as Research Assistant<br />
**Jungha Lee, went to graduate school (2017 summer), went to graduate school (Seoul National Univ.)<br />
**Seunghyun Wang, went to graduate school (2017 summer) went to graduate school (KAIST)<br />
**Dong-Min Yang (2017 fall)<br />
**Doo-Hee Lee (2017 fall)<br />
**Suk-Jae Han (2018 winter)<br />
**Ji-Eun Han (2018 winter)<br />
**Yuri Ko (2018 spring)<br />
**Sung-Woo Kim (2018 spring)<br />
**Woosung Kwon (2018 summer)<br />
**Soyun Kong (2018 summer)<br />
**Hojeong Keum (2018 summer and fall)<br />
**Sungjun Lim (2018 summer and fall)<br />
**Jiyoon Lee (2018 summer and fall)<br />
**Junik Park (2019 winter)<br />
**Lee Yoo (2019 winter & spring)<br />
**Yeonwha Kim (2019 winter & spring)<br />
**Sohee Kim (2019 spring)<br />
**Juseong Lee (2019 spring)<br />
**Junyoung Yang (2019 summer)<br />
**Junyoung Ma (2019 summer)<br />
**Dayun Jung (2019 summer)<br />
**Hanjoon Kim (2019 summer)</div>
Administrator
https://netbiolab.org/w/Welcome
Welcome
2019-08-23T01:55:52Z
<p>Administrator: </p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
|colspan="3"|<br />
<div style="font-size:225%;font-weight:1000;">Welcome to Network Biomedicine Laboratory</div><br />
<br />
|-<br />
|rowspan="2" style="padding-right:20px;"|<br />
[[File:Web_main_2019.png|center|780px]]<br />
<br />
|colspan=2|<br />
<br />
=== Research Keyword Cloud (2013-2017)===<br />
<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><br />
<br />
|-<br />
|<br />
=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| KS Kim<br />
|style="width:65px"| CY Kim<br />
|-<br />
|JW Cho<br />
|SH Lee<br />
|-<br />
|JH Cha<br />
|NY Kim<br />
|-<br />
|SB Baek<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>
Administrator
https://netbiolab.org/w/Publications
Publications
2019-05-22T11:04:13Z
<p>Administrator: </p>
<hr />
<div>* [http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]<br />
* [https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]<br />
* [http://www.researcherid.com/rid/F-7722-2010 {{#widget:AddHtml|content=<img src='https://labs.researcherid.com/mashlets/badge/rid-idsymbol4.gif' border='0' />}}]<br />
* '*' First authors; '**' Corresponding authors; <br />
==2020== <br />
*85. Lee T*, '''Lee I**''' Genome-wide Association Studies in Arabidopsis thaliana: Statistical Analysis and Network-Based Augmentation of Signals '''''Arabidopsis Protocols 4th Ed.''''' [https://netbiolab.org/wiki/glucose_germrate.txt Supplementary File] submitted<br />
<br><br />
<br />
==2019== <br />
*84. Single-cell transcriptome analysis revealed a role of the transcription factor TOX in promoting CD8+ T-cell exhaustion in cancer '''''Preprint''''' 2019 May 18. [https://www.biorxiv.org/content/10.1101/641316v1 bioXriv] <br />
<br><br />
*83. Shim JE**, '''Lee I**''', Construction of functional protein networks using domain profile associations, '''''Methods in Molecular Biology''''' In press<br />
<br><br />
*82. NGSEA: network-based gene set enrichment analysis for interpreting gene expression phenotypes with functional gene sets '''''Preprint''''' 2019 May 15. [https://www.biorxiv.org/content/10.1101/636498v1 bioXriv]<br />
<br><br />
*81. Network integrative genomic and transcriptomic analysis of carbapenem-resistant Klebsiella pneumoniae strains identifies genes for antibiotic-resistance and virulence '''''mSystems''''' In press<br />
<br><br />
*80. Shim JE*, Kim JH, Shin J, Lee JE, '''Lee I**''' Pathway-specific protein domains are predictive for human diseases '''''PLOS Computational Biology''''' 2019 May 10;15(5):e1007052 [https://www.ncbi.nlm.nih.gov/pubmed/31075101 pubmed] <br />
<br><br />
*79. Lee T*, Lee S*, Yang S, '''Lee I**'''. MaizeNet: A co-functional network for network-assisted systems genetics in Zea mays '''''The Plant Journal''''' 2019 Apr 21. doi: 10.1111/tpj.14341 [https://www.ncbi.nlm.nih.gov/pubmed/31006149 pubmed]<br />
<br><br />
*78. Kim H*, Joe A*, Lee M, Yang S, Ma X, Ronald PC**, '''Lee I**'''. A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems '''''Mol Cells''''' 2019 Feb 28;42(2):166-174 [https://www.ncbi.nlm.nih.gov/pubmed/30759970 pubmed]<br />
<br><br />
*77. Hwang S*, Kim CY*, Yang S, Kim E, Hart T, Marcotte EM, '''Lee I**'''. HumanNet v2: human gene networks for disease research '''''Nucleic Acids Research''''' 2019 Jan 8;47(D1):D573–D580.[https://www.ncbi.nlm.nih.gov/pubmed/30418591 pubmed]<br />
<br><br />
<br />
==2018 (5)== <br />
*76. Han H*, Lehner B, '''Lee I**''', Cancer gene discovery by network analysis of somatic mutations using the MUFFINN server, '''''Methods in Molecular Biology''''' 2018 Dec 13; 1907:37-50.[https://www.ncbi.nlm.nih.gov/pubmed/30542989 pubmed]<br />
<br><br />
*75. 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. [https://www.ncbi.nlm.nih.gov/pubmed/30018396 pubmed]<br />
<br><br />
*74. Lim KT, Kim J, Hwang SI, Zhang L, Han H, Bae D, Kim KP, Hu YP, Schöler HR, '''Lee I''', Hui L, Han DW, Direct Conversion of Mouse Fibroblasts into Cholangiocyte Progenitor Cells. '''''Stem Cell Reports''''' 2018 Mar 27. 10:1-15.[https://www.ncbi.nlm.nih.gov/pubmed/29606616 pubmed]<br />
<br><br />
*73. Lee T*, '''Lee I**''', araGWAB: A web application for network-based boosting of genome-wide association signals in Arabidopsis '''''Scientific Reports''''' 2018 Feb 13;8(1):2925.[https://www.ncbi.nlm.nih.gov/pubmed/29440686 pubmed]<br />
<br><br />
*72. Han H*, Cho JW, Lee S, Yun A, Kim H, Bae D, Yang S, Kim CY, Lee M, Kim E, Lee S, Kang B, Jeong D, Kim Y, Jeon HN, Jung H, Nam S, Chung M, Kim JH, '''Lee I**''', TRRUST v2: An expanded reference database of human and mouse transcriptional regulatory interactions '''''Nucleic Acids Research''''' 2018 Jan 4;46(D1):D380–D386.[https://www.ncbi.nlm.nih.gov/pubmed/29087512 pubmed]<br />
<br><br />
<br />
==2017 (10)== <br />
*71. Kim CY*, '''Lee I**''', Functional gene networks based on the gene neighborhood in metagenomes, '''''Animal Cells and Systems''''' 2017 Sept 29; 21:301-306; <br />
<br><br />
*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] <br />
<br><br />
*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]<br />
<br><br />
*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 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]<br />
<br><br />
*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 />}}]<br />
<br><br />
*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; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
<br />
==2016 (10)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
<br />
==2015 (14)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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 />}}]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
==2014 (5)-Sabbatical leave==<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 />
<br><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 />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
==2013 (2)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
==2012 (3)==<br />
*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] <br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
==2011 (5)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
==2010 (4)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
==2009 (3)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
==2008 (3)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<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><br />
==Before 2007 (12)==<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><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><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><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><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><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><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><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><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><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><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><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 />
<br></div>
Administrator
https://netbiolab.org/w/Publications
Publications
2019-05-22T10:39:58Z
<p>Administrator: </p>
<hr />
<div>* [http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]<br />
* [https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]<br />
* [http://www.researcherid.com/rid/F-7722-2010 {{#widget:AddHtml|content=<img src='https://labs.researcherid.com/mashlets/badge/rid-idsymbol4.gif' border='0' />}}]<br />
* '*' First authors; '**' Corresponding authors; <br />
==2020== <br />
*85. Lee T*, '''Lee I**''' Genome-wide Association Studies in Arabidopsis thaliana: Statistical Analysis and Network-Based Augmentation of Signals '''''Arabidopsis Protocols 4th Ed.''''' [https://netbiolab.org/wiki/images/e/eb/Glucose_germrate.txt Supplementary File] submitted<br />
<br><br />
<br />
==2019== <br />
*84. Single-cell transcriptome analysis revealed a role of the transcription factor TOX in promoting CD8+ T-cell exhaustion in cancer '''''Preprint''''' 2019 May 18. [https://www.biorxiv.org/content/10.1101/641316v1 bioXriv] <br />
<br><br />
*83. Shim JE**, '''Lee I**''', Construction of functional protein networks using domain profile associations, '''''Methods in Molecular Biology''''' In press<br />
<br><br />
*82. NGSEA: network-based gene set enrichment analysis for interpreting gene expression phenotypes with functional gene sets '''''Preprint''''' 2019 May 15. [https://www.biorxiv.org/content/10.1101/636498v1 bioXriv]<br />
<br><br />
*81. Network integrative genomic and transcriptomic analysis of carbapenem-resistant Klebsiella pneumoniae strains identifies genes for antibiotic-resistance and virulence '''''mSystems''''' In press<br />
<br><br />
*80. Shim JE*, Kim JH, Shin J, Lee JE, '''Lee I**''' Pathway-specific protein domains are predictive for human diseases '''''PLOS Computational Biology''''' 2019 May 10;15(5):e1007052 [https://www.ncbi.nlm.nih.gov/pubmed/31075101 pubmed] <br />
<br><br />
*79. Lee T*, Lee S*, Yang S, '''Lee I**'''. MaizeNet: A co-functional network for network-assisted systems genetics in Zea mays '''''The Plant Journal''''' 2019 Apr 21. doi: 10.1111/tpj.14341 [https://www.ncbi.nlm.nih.gov/pubmed/31006149 pubmed]<br />
<br><br />
*78. Kim H*, Joe A*, Lee M, Yang S, Ma X, Ronald PC**, '''Lee I**'''. A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems '''''Mol Cells''''' 2019 Feb 28;42(2):166-174 [https://www.ncbi.nlm.nih.gov/pubmed/30759970 pubmed]<br />
<br><br />
*77. Hwang S*, Kim CY*, Yang S, Kim E, Hart T, Marcotte EM, '''Lee I**'''. HumanNet v2: human gene networks for disease research '''''Nucleic Acids Research''''' 2019 Jan 8;47(D1):D573–D580.[https://www.ncbi.nlm.nih.gov/pubmed/30418591 pubmed]<br />
<br><br />
<br />
==2018 (5)== <br />
*76. Han H*, Lehner B, '''Lee I**''', Cancer gene discovery by network analysis of somatic mutations using the MUFFINN server, '''''Methods in Molecular Biology''''' 2018 Dec 13; 1907:37-50.[https://www.ncbi.nlm.nih.gov/pubmed/30542989 pubmed]<br />
<br><br />
*75. 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. [https://www.ncbi.nlm.nih.gov/pubmed/30018396 pubmed]<br />
<br><br />
*74. Lim KT, Kim J, Hwang SI, Zhang L, Han H, Bae D, Kim KP, Hu YP, Schöler HR, '''Lee I''', Hui L, Han DW, Direct Conversion of Mouse Fibroblasts into Cholangiocyte Progenitor Cells. '''''Stem Cell Reports''''' 2018 Mar 27. 10:1-15.[https://www.ncbi.nlm.nih.gov/pubmed/29606616 pubmed]<br />
<br><br />
*73. Lee T*, '''Lee I**''', araGWAB: A web application for network-based boosting of genome-wide association signals in Arabidopsis '''''Scientific Reports''''' 2018 Feb 13;8(1):2925.[https://www.ncbi.nlm.nih.gov/pubmed/29440686 pubmed]<br />
<br><br />
*72. Han H*, Cho JW, Lee S, Yun A, Kim H, Bae D, Yang S, Kim CY, Lee M, Kim E, Lee S, Kang B, Jeong D, Kim Y, Jeon HN, Jung H, Nam S, Chung M, Kim JH, '''Lee I**''', TRRUST v2: An expanded reference database of human and mouse transcriptional regulatory interactions '''''Nucleic Acids Research''''' 2018 Jan 4;46(D1):D380–D386.[https://www.ncbi.nlm.nih.gov/pubmed/29087512 pubmed]<br />
<br><br />
<br />
==2017 (10)== <br />
*71. Kim CY*, '''Lee I**''', Functional gene networks based on the gene neighborhood in metagenomes, '''''Animal Cells and Systems''''' 2017 Sept 29; 21:301-306; <br />
<br><br />
*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] <br />
<br><br />
*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]<br />
<br><br />
*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 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]<br />
<br><br />
*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 />}}]<br />
<br><br />
*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; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
<br />
==2016 (10)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
<br />
==2015 (14)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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 />}}]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
==2014 (5)-Sabbatical leave==<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 />
<br><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 />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
*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]<br />
<br><br />
==2013 (2)==<br />
*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]<br />
<br><br />
*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]<br />
<br><br />
==2012 (3)==<br />
*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] <br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
==2011 (5)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
==2010 (4)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
==2009 (3)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
==2008 (3)==<br />
*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]]<br />
<br><br />
*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]]<br />
<br><br />
*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]]<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><br />
==Before 2007 (12)==<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><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><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><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><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><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><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><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><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><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><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><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 />
<br></div>
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<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
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<div style="font-size:225%;font-weight:1000; padding:.1em;">Welcome to Network Biomedicine Laboratory</div><br />
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=== Research Keyword Cloud (2013-2017)===<br />
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=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| HJ Han<br />
|style="width:65px"| KS Kim<br />
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|CY Kim<br />
| DS Bae<br />
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| JW Cho<br />
| SH Lee<br />
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=== Visitors Trend ===<br />
[https://www.clustrmaps.com/map/Netbiolab.org https://www.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]<br />
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===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 />
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[공지사항] <sup>2019 겨울학기</sup> [[연세 MRC 시스템의학연구센터 네트워크생명공학연구실 인턴연구원 모집]]<br />
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__NOTOC__<br />
{|border = "0" valign="top"<br />
|colspan="3"|<br />
<div style="font-size:225%;font-weight:1000; padding:.5em;">Welcome to Network Biomedicine Laboratory</div><br />
<br />
|-<br />
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[[File:2018_%EB%9E%A9%EB%8B%A8%EC%B2%B4%EC%82%AC%EC%A7%84.jpg|center|680px]]<br />
<br />
|colspan=2|<br />
=== Research Keyword Cloud (2013-2017)===<br />
<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><br />
<br />
|-<br />
|<br />
=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| HJ Han<br />
|style="width:65px"| KS Kim<br />
|-<br />
|CY Kim<br />
| DS Bae<br />
|-<br />
| JW Cho<br />
| SH Lee<br />
|-<br />
|}<br />
|<br />
=== Visitors Trend ===<br />
[https://www.clustrmaps.com/map/Netbiolab.org https://www.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]<br />
|-<br />
|colspan=3|<br />
===Contact Informations===<br />
<pre><br />
Yonsei University <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>
Administrator
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연세 MRC 시스템의학연구센터 네트워크생명공학연구실 인턴연구원 모집
2018-10-23T05:16:56Z
<p>Administrator: Created page with "frameless"</p>
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https://netbiolab.org/w/Research
Research
2018-02-26T08:56:30Z
<p>Administrator: </p>
<hr />
<div>=='''Research Summary'''==<br />
<div style="float:right;margin:5px 40px;">{{#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><br />
<div style="text-align:justify;"><br />
'''Network Medicine via network-augmented analysis of clinical genomics data'''<br />
<br />
Recent genomic revolution opened new avenues to understanding human disease. However, it also revealed complex nature of human disease. For example, currently, more than several hundred genes are believed to be associated with human cancer. Genome-wide association study (GWAS) suggests hundreds of disease-related genes, but together explaining only 10-20% of total disease inheritance at most. Because of this overwhelming complexity of disease-causing pathway, modern disease genetics needs to be more systematic and predictive. However, the network organization of disease systems also provide big opportunity to investigate the genetic organization of complex diseases through the molecular networks. Our research group has developed co-functional gene networks for many organisms including human (HumanNet) and various network-guided methods to identify novel disease genes and modules. <br />
.</div><br />
<br />
=='''Research Highlight'''==<br />
*[[media:research_highlight_004.pdf|2011 Nature Reviews Genetics, Research highlight (Predicting genetic interaction)]]<br />
*[[media:research_highlight_002.pdf|2008 Bioessay, What the papers say (WormNet)]]<br />
*[[media:research_highlight_003.pdf|2008 Genome Biology, Minireview (WormNet)]]<br />
*[[media:research_highlight_001.pdf|2008 Nature methods, Research highlight (WormNet)]]<br />
*[[media:Gallery_NGcover_SmallVer.jpg|2008 Nature Genetics coverstory (WormNet): Network perturbation predicts phenotype]]</div>
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https://netbiolab.org/w/MediaWiki:Mainpage
MediaWiki:Mainpage
2018-02-26T08:54:12Z
<p>Administrator: </p>
<hr />
<div>Welcome</div>
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2018-02-26T08:52:03Z
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<div>* Navigation<br />
** Welcome|Main page<br />
** Research|Research<br />
** Publications|Publications<br />
** Software|Software<br />
** People|People<br />
** Album|Album<br />
** Journal Club|Journal Club<br />
** Favorite Journals|Favorite Journals<br />
** Web Resources|Web Resources<br />
** Protocols | Protocols<br />
** Media & Outreach|Media & Outreach<br />
** Positions Available|Positions Available<br />
** Teaching | Teaching<br />
* SEARCH<br />
* TOOLBOX<br />
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<div>* Navigation<br />
** Welcome| Main page<br />
** Research|Research<br />
** Publications|Publications<br />
** Software|Software<br />
** People|People<br />
** Album|Album<br />
** Journal Club|Journal Club<br />
** Favorite Journals|Favorite Journals<br />
** Web Resources|Web Resources<br />
** Protocols | Protocols<br />
** Media & Outreach|Media & Outreach<br />
** Positions Available|Positions Available<br />
** Teaching | Teaching<br />
* SEARCH<br />
* TOOLBOX<br />
* LANGUAGES</div>
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https://netbiolab.org/w/Welcome
Welcome
2018-02-26T08:49:34Z
<p>Administrator: Created page with "__NOTOC__ {|border = "0" valign="top" |colspan="3"| <div style="font-size:225%;font-weight:1000; padding:.1em;">Welcome to Network Biomedicine Laboratory</div> |- |rowspan="..."</p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
|colspan="3"|<br />
<div style="font-size:225%;font-weight:1000; padding:.1em;">Welcome to Network Biomedicine Laboratory</div><br />
<br />
|-<br />
|rowspan="2" style="padding-right:20px;"|<br />
[[File:Groupphoto 20161208 crop.jpg|center|680px]]<br />
<br />
|colspan=2|<br />
=== Research Keyword Cloud (2013-2017)===<br />
<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><br />
<br />
|-<br />
|<br />
=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| HJ Han<br />
|style="width:65px"| KS Kim<br />
|-<br />
|CY Kim<br />
| DS Bae<br />
|-<br />
| JW Cho<br />
| SH Lee<br />
|-<br />
|}<br />
|<br />
=== Visitors Trend ===<br />
[https://www.clustrmaps.com/map/Netbiolab.org https://www.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]<br />
|-<br />
|colspan=3|<br />
===Contact Informations===<br />
<pre><br />
Yonsei University <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>
Administrator
https://netbiolab.org/w/MediaWiki:Common.css
MediaWiki:Common.css
2018-02-26T07:56:11Z
<p>Administrator: </p>
<hr />
<div>/* CSS placed here will be applied to all skins */<br />
body.page-Main_Page.action-view h1.firstHeading, body.page-Main_Page.action-submit h1.firstHeading { display: none; }<br />
body.page-Welcome.action-view h1.firstHeading,<br />
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2018-02-26T07:53:31Z
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2018-02-26T07:51:56Z
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2018-02-26T07:48:34Z
<p>Administrator: Created page with "/* CSS placed here will be applied to all skins */ body.page-Main_Page.action-view h1.firstHeading, body.page-Main_Page.action-submit h1.firstHeading { display: none; }"</p>
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body.page-Main_Page.action-view h1.firstHeading, body.page-Main_Page.action-submit h1.firstHeading { display: none; }</div>
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https://netbiolab.org/w/Software
Software
2017-03-04T02:50:08Z
<p>Administrator: </p>
<hr />
<div>__NOTOC__<br />
=='''Co-functional networks and hypothesis generation servers'''==<br />
<br />
==''Human and Animals''==<br />
{|border="0" width="500"<br />
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]<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"|''Homo sapiens''<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:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]<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 />
|align="center"|[[File:WheatNet_logo.png|150px|link=http://www.inetbio.org/wheatnet]]<br />
|-<br />
|align="center"|''Arabidopsis thaliana''<br />
|align="center"|''Oryza sativa''<br />
|align="center"|''Glycine max''<br />
|align="center"|''Solanum lycopersicum''<br />
|align="center"|''Triticum aestivum''<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: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''<br />
|align="center"|''Escherichia coli''<br />
|align="center"|''Xanthomonas oryzae pv. oryzae''<br />
|}<br />
<br />
<br />
<br />
<br />
=='''Build your co-functional networks for all other species'''==<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-based servers for Disease Research'''==<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: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:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN (MUtations For Functional Impact on Network Neighbors): cancer gene discovery via network analysis of somatic mutation data'''<br />
<br />
<br />
<br />
[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN (Model Organisms Projected on a Human Integrated Gene Network): Network-assisted prediction of disease pathways in model organisms'''<br />
<br />
<br />
<br />
<br />
<br />
<br />
=='''Other Network Biology tools'''==<br />
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST (Transcriptional Regulatory relationships Unraveled by Sentence-based Text mining): A reference database of human TF-target interactions'''<br />
<br />
<br />
<br />
[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE (Reflective diffusion and local extension): Network-assisted Gene Set Analysis (human only)'''<br />
<br />
<br />
<br />
<br />
<br />
<br />
=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==<br />
[[WMI|<big>'''Project Page'''</big>]]</div>
Administrator
https://netbiolab.org/w/File:GWAB_logo.png
File:GWAB logo.png
2017-03-04T02:40:34Z
<p>Administrator: </p>
<hr />
<div></div>
Administrator
https://netbiolab.org/w/File:WheatNet_logo.png
File:WheatNet logo.png
2017-03-04T02:40:25Z
<p>Administrator: </p>
<hr />
<div></div>
Administrator
https://netbiolab.org/w/File:XooNet_logo.png
File:XooNet logo.png
2017-03-04T02:40:08Z
<p>Administrator: </p>
<hr />
<div></div>
Administrator
https://netbiolab.org/w/Software
Software
2017-01-03T01:30:53Z
<p>Administrator: /* Plants */</p>
<hr />
<div>__NOTOC__<br />
=='''Co-functional networks and hypothesis generation servers'''==<br />
<br />
==''Human and Animals''==<br />
{|border="0" width="800"<br />
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]<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"|''Homo sapiens''<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="500"<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 />
|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"|''Oryza sativa''<br />
|align="center"|''Glycine max''<br />
|align="center"|''Solanum lycopersicum''<br />
|}<br />
<br />
==''Fungi''==<br />
{|border="0" width="400"<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="400"<br />
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]]<br />
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]<br />
|-<br />
|align="center"|''Pseudomonas aeruginosa''<br />
|align="center"|''Escherichia coli''<br />
|}<br />
<br />
<br />
=='''Build your co-functional networks for all other species'''==<br />
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]] '''JiffyNet:Instant gene network building server for newly sequenced species'''<br />
<br />
<br />
<br />
<br />
<br />
<br />
=='''Network-based servers for Disease Research'''==<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 />
<br />
[[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN (MUtations For Functional Impact on Network Neighbors): cancer gene discovery via network analysis of somatic mutation data'''<br />
<br />
<br />
<br />
[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN (Model Organisms Projected on a Human Integrated Gene Network): Network-assisted prediction of disease pathways in model organisms'''<br />
<br />
<br />
<br />
<br />
<br />
<br />
=='''Other Network Biology tools'''==<br />
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST (Transcriptional Regulatory relationships Unraveled by Sentence-based Text mining): A reference database of human TF-target interactions'''<br />
<br />
<br />
<br />
[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE (Reflective diffusion and local extension): Network-assisted Gene Set Analysis (human only)'''<br />
<br />
<br />
<br />
<br />
<br />
<br />
=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==<br />
[[WMI|<big>'''Project Page'''</big>]]</div>
Administrator
https://netbiolab.org/w/File:Tomatonet_logo.png
File:Tomatonet logo.png
2017-01-03T01:30:37Z
<p>Administrator: </p>
<hr />
<div></div>
Administrator
https://netbiolab.org/w/Research
Research
2016-12-13T09:45:34Z
<p>Administrator: </p>
<hr />
<div>=='''Research Summary'''==<br />
<div style="float:right;margin:5px 40px;">{{#widget:AddHtml|content=<img src="../wiki/cloud2.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div><br />
<div style="text-align:justify;"><br />
The ultimate goal of biological research is to manipulate traits that are important for medicine, agriculture, and bio-industry. This challenging task first requires good understanding of association between genotype and phenotype. Because of high complexity of genotype as well as phenotype, complexity of the genotype-phenotype association could be even untouchable by combinatorial explosion of the number of possible associations. Therefore, modern genetics needs to be more systematic and predictive. Recently we proposed network-guided approach for genetics of complex traits. First, we construct probabilistic functional gene networks for cells or organisms by benchmarking and integrating heterogeneous multi-omics data that are in general publicly available. Then, using guilt-by-association, and other algorithms of network propagation of known biological information, we predict gene functions, phenotypic effect of loss-of-function, and epistatic interaction. The information can contribute to reconstruction of map between genotype and phenotype. The network-guided genetics method has been effectively applied for various organisms; from simple microbe yeast, to multicellular animal C. elegans, to the reference plant Arabidopsis, to the reference crop rice, and to the human.</div><br />
<br />
=='''Research Highlight'''==<br />
*[[media:research_highlight_004.pdf|2011 Nature Reviews Genetics, Research highlight (Predicting genetic interaction)]]<br />
*[[media:research_highlight_002.pdf|2008 Bioessay, What the papers say (WormNet)]]<br />
*[[media:research_highlight_003.pdf|2008 Genome Biology, Minireview (WormNet)]]<br />
*[[media:research_highlight_001.pdf|2008 Nature methods, Research highlight (WormNet)]]<br />
*[[media:Gallery_NGcover_SmallVer.jpg|2008 Nature Genetics coverstory (WormNet): Network perturbation predicts phenotype]]</div>
Administrator
https://netbiolab.org/w/Welcome_to_Network_Biology_Laboratory
Welcome to Network Biology Laboratory
2016-12-12T10:41:46Z
<p>Administrator: </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 ===<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 />
=== 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>
Administrator
https://netbiolab.org/w/Publications
Publications
2016-07-13T11:00:22Z
<p>Administrator: </p>
<hr />
<div>* [http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]<br />
* [http://www.researcherid.com/rid/F-7722-2010 {{#widget:AddHtml|content=<img src='https://labs.researcherid.com/mashlets/badge/rid-idsymbol4.gif' border='0' />}}]<br />
* '*' co-corresponding authorship<br />
==2016 (7)==<br />
*58. 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 May 4. pii: jbc.M115.713578. [http://www.ncbi.nlm.nih.gov/pubmed/27189941 pubmed]<br />
*57. Shim JE, '''Lee I''' Weighted mutual information analysis substantially improves domain-based functional network models. '''''Bioinformatics''''' 2016 May 20. pii: btw320 [http://www.ncbi.nlm.nih.gov/pubmed/27207946 pubmed]<br />
*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]<br />
*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]<br />
*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]<br />
*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]<br />
*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]<br />
<br />
==2015 (14)==<br />
<br />
*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]<br />
*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]<br />
*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]]<br />
*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]<br />
*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]<br />
*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]<br />
*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]<br />
*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]<br />
*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]<br />
*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-asisted 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]<br />
*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]<br />
*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]<br />
*39. Kim H, Shim JE, Shin J, '''Lee I''', EcoliNet: a database of cofunctional gene network for Escherichia coli, '''''Database''''' 2015 Feb 2;2015 [http://www.ncbi.nlm.nih.gov/pubmed/25650278 Pubmed]<br />
*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]<br />
<br />
==2014 (5)==<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. 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]<br />
*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]<br />
*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]<br />
<br />
==2013 (2)==<br />
*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]<br />
*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]<br />
<br />
==2012 (3)==<br />
*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] <br />
*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]]<br />
*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]]<br />
<br />
==2011 (5)==<br />
*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]]<br />
<br />
*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]]<br />
<br />
*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]]<br />
<br />
*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]]<br />
<br />
*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]]<br />
<br />
==2010 (4)==<br />
*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]]<br />
<br />
*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]]<br />
<br />
*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]]<br />
<br />
*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]]<br />
<br />
==2009 (3)==<br />
*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]]<br />
<br />
*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]]<br />
<br />
*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]]<br />
<br />
==2008 (3)==<br />
*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]]<br />
<br />
*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]]<br />
<br />
*13. '''Lee I''', Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM.Lee I1, 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]]<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 (12)==<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)</div>
Administrator
https://netbiolab.org/w/Welcome_to_Network_Biology_Laboratory
Welcome to Network Biology Laboratory
2016-07-13T10:58:34Z
<p>Administrator: </p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
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[[File :P4070576 2.jpg|580px|center|middle|Main Photo]]<br />
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=== Research Keyword Cloud ===<br />
<div>{{#widget:AddHtml|content=<img src="../wiki/cloud.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div><br />
|-<br />
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=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| JE Shim<br />
|style="width:65px"| T Lee<br />
|style="width:65px"| HJ Han<br />
|-<br />
| KS Kim<br />
| ER Kim<br />
| CY Kim*<br />
|-<br />
| DS Bae<br />
| SM Yang<br />
| MY Lee<br />
|}<br />
|<br />
<br />
=== Visitors Trend ===<br />
[https://www.clustrmaps.com/map/Netbiolab.org https://www.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]<br />
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===Contact Informations===<br />
<pre><br />
Yonsei University 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea <br />
Office: Engineering Research Park B118DA<br />
+82-70-8625-5205 <br />
</pre><br />
|}</div>
Administrator
https://netbiolab.org/w/Journal_Club
Journal Club
2016-06-01T00:31:52Z
<p>Administrator: </p>
<hr />
<div>{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2016<br />
|-<br />
!scope="col" style="padding:.4em" |Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/8<br />
|style="padding:.4em;"|2016-12<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26619012 Mapping the effects of drugs on the immune system]<br />
|-<br />
|style="padding:.4em;"| 2016-11<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26186195 Elucidating compound mechanism of action by network perturbation analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/6/1<br />
|style="padding:.4em;"|2016-10<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26854917 Integrative approaches for large-scale transcriptome-wide association studies]<br />
|-<br />
|style="padding:.4em;"| 2016-9<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26950747 Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/18<br />
|style="padding:.4em;"|2016-8<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/27013732 Survey of variation in human transcription factors reveals prevalent DNA binding changes]<br />
|-<br />
|style="padding:.4em;"| 2016-7<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26502339 Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/11<br />
|style="padding:.4em;"|2016-6<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25171417 Predicting Cancer-specific vulnerability via data-driven detection of synthetic lethality]<br />
|-<br />
|style="padding:.4em;"| 2016-5<br />
|style="padding:.4em;"|DS Bae, CY Kim <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23467089 Dynamic regulatory network controlling Th17 cell differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/5/4<br />
|style="padding:.4em;"|2016-4<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25853550 Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy]<br />
|-<br />
|style="padding:.4em;"| 2016-3<br />
|style="padding:.4em;"|MY Lee,SM Cho <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26618344 Regulators of genetic risk of breast cancer identified by integrative network analysis]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2016/4/27<br />
|style="padding:.4em;"|2016-2<br />
|style="padding:.4em;"|CY Kim,SJ Kwon<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/26780608 A predictive computational framework for direct reprogramming between human cell types]<br />
|-<br />
|style="padding:.4em;"| 2016-1<br />
|style="padding:.4em;"| CY Kim,SJ Kwon <br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/25126793 CellNet: Network biology applied to stem cell engineering]<br />
|}<br />
<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2015<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/11<br />
|style="padding:.4em;"|2015-55<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/24/2/340.long Improved exome prioritization of disease genes through cross-species phenotype comparison.]<br />
|-<br />
|style="padding:.4em;"|2015-54<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0002929714001128 Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/06/04<br />
|style="padding:.4em;"|2015-53<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2656.html eXtasy: variant prioritization by genomic data fusion.]<br />
|-<br />
|style="padding:.4em;"|2015-52<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/21/9/1529.long A probabilistic disease-gene finder for personal genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/28<br />
|style="padding:.4em;"|2015-51<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n12/full/ng.3141.html Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2015-50<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v28/n5/full/nbt.1630.html GREAT improves functional interpretation of cis-regulatory regions.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/21<br />
|style="padding:.4em;"|2015-49<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2832.html Functional annotation of noncoding sequence variants.]<br />
|-<br />
|style="padding:.4em;"|2015-48<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/15/10/480 FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/05/14<br />
|style="padding:.4em;"|2015-47<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3215.html Selecting causal genes from genome-wide association studies via functionally coherent subnetworks.]<br />
|-<br />
|style="padding:.4em;"|2015-46<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2015/150119/ncomms6890/full/ncomms6890.html Biological interpretation of genome-wide association studies using predicted gene functions.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/05/07<br />
|style="padding:.4em;"|2015-45<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/140626/ncomms5212/full/ncomms5212.html Human symptoms-disease network.]<br />
|-<br />
|style="padding:.4em;"|2015-44<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413010246 A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.]<br />
|-<br />
|style="padding:.4em;"|2015-43<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6224/1257601.long Uncovering disease-disease relationships through the incomplete interactome.]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/30<br />
|style="padding:.4em;"|2015-42<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/142.long The discovery of integrated gene networks for autism and related disorders.]<br />
|-<br />
|style="padding:.4em;"|2015-41<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/12/774.long Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/04/23<br />
|style="padding:.4em;"|2015-40<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature13990.html Dissecting neural differentiation regulatory networks through epigenetic footprinting.]<br />
|-<br />
|style="padding:.4em;"|2015-39<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Cell-of-origin chromatin organization shapes the mutational landscape of cancer.]<br />
|-<br />
|style="padding:.4em;"|2015-38<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v518/n7539/full/nature14248.html Integrative analysis of 111 reference human epigenomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/09<br />
|style="padding:.4em;"|2015-37<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/246.long Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.]<br />
|-<br />
|style="padding:.4em;"|2015-36<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014974 A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/04/02<br />
|style="padding:.4em;"|2015-35<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.]<br />
|-<br />
|style="padding:.4em;"|2015-34<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/347/6225/1010.long Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/26<br />
|style="padding:.4em;"|2015-33<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/2/257.long Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.]<br />
|-<br />
|style="padding:.4em;"|2015-32<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/25/1/41.long Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/03/19<br />
|style="padding:.4em;"|2015-31<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3154.html Decoding the regulatory network of early blood development from single-cell gene expression measurements.]<br />
|-<br />
|style="padding:.4em;"|2015-30<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v16/n3/full/nrg3833.html Computational and analytical challenges in single-cell transcriptomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/12<br />
|style="padding:.4em;"|2015-29<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867415000136 Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.]<br />
|-<br />
|style="padding:.4em;"|2015-28<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v500/n7464/full/nature12506.html Richness of human gut microbiome correlates with metabolic markers.]<br />
|-<br />
|style="padding:.4em;"|2015-27<br />
|style="padding:.4em;"|<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v490/n7418/full/nature11450.html A metagenome-wide association study of gut microbiota in type 2 diabetes.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/09<br />
|style="padding:.4em;"|2015-26<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326 Practical guidelines for the comprehensive analysis of ChIP-seq data.]<br />
|-<br />
|style="padding:.4em;"|2015-25<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/5/777.long Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.]<br />
|-<br />
|style="padding:.4em;"|2015-24<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/11/760.long Rapid neurogenesis through transcriptional activation in human stem cells.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/03/02<br />
|style="padding:.4em;"|2015-23<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414011787 Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.]<br />
|-<br />
|style="padding:.4em;"|2015-22<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004237 Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.]<br />
|-<br />
|style="padding:.4em;"|2015-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html The Genotype-Tissue Expression (GTEx) project.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/24<br />
|style="padding:.4em;"|2015-20<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/346/6212/1007.long Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.]<br />
|-<br />
|style="padding:.4em;"|2015-19<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13985.html Principles of regulatory information conservation between mouse and human.]<br />
|-<br />
|style="padding:.4em;"|2015-18<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v515/n7527/full/nature13972.html Conservation of trans-acting circuitry during mammalian regulatory evolution.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/02/16<br />
|style="padding:.4em;"|2015-17<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13835.html Genetic and epigenetic fine mapping of causal autoimmune disease variants.]<br />
|-<br />
|style="padding:.4em;"|2015-16<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n3/full/ng.2892.html A general framework for estimating the relative pathogenicity of human genetic variants.]<br />
|-<br />
|style="padding:.4em;"|2015-15<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825 A probabilistic model to predict clinical phenotypic traits from genome sequencing.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2015/02/02<br />
|style="padding:.4em;"|2015-14<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/22/E2329.long Relating the metatranscriptome and metagenome of the human gut.]<br />
|-<br />
|style="padding:.4em;"|2015-13<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v513/n7516/full/nature13568.html Alterations of the human gut microbiome in liver cirrhosis.]<br />
|-<br />
|style="padding:.4em;"|2015-12<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2942.html An integrated catalog of reference genes in the human gut microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-11<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/v32/n8/full/nbt.2939.html Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.]<br />
|-<br />
|style="padding:.4em;" rowspan=5|2015/01/26<br />
|style="padding:.4em;"|2015-10<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/9/1/666.long Computational meta'omics for microbial community studies.]<br />
|-<br />
|style="padding:.4em;"|2015-09<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/5/7/65 Functional profiling of the gut microbiome in disease-associated inflammation.]<br />
|-<br />
|style="padding:.4em;"|2015-08<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S016895251200145X Biodiversity and functional genomics in the human microbiome.]<br />
|-<br />
|style="padding:.4em;"|2015-07<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002808 Chapter 12: Human Microbiome Analysis.]<br />
|-<br />
|style="padding:.4em;"|2015-06<br />
|style="padding:.4em;"|BH Kang<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.cell.com/cell/abstract/S0092-8674%2814%2900864-2 Conducting a Microbiome Study.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2015/01/12<br />
|style="padding:.4em;"|2015-05<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ncomms/2014/141210/ncomms6522/full/ncomms6522.html Small RNA changes en route to distinct cellular states of induced pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-04<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html Genome-wide characterization of the routes to pluripotency.]<br />
|-<br />
|style="padding:.4em;"|2015-03<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html Divergent reprogramming routes lead to alternative stem-cell states.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2015/01/05<br />
|style="padding:.4em;"|2015-02<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/111/21/E2191.long Global view of enhancer-promoter interactome in human cells.]<br />
|-<br />
|style="padding:.4em;"|2015-01<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://nar.oxfordjournals.org/content/41/22/10391.long Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2014<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/23<br />
|style="padding:.4em;"|2014-41<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413012270 Super-enhancers in the control of cell identity and disease.]<br />
|-<br />
|style="padding:.4em;"|2014-40<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867413003929 Master transcription factors and mediator establish super-enhancers at key cell identity genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=4|2014/12/09<br />
|style="padding:.4em;"|2014-39<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414013713 Unraveling the biology of a fungal meningitis pathogen using chemical genetics.]<br />
|-<br />
|style="padding:.4em;"|2014-38<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414014226 A proteome-scale map of the human interactome network.]<br />
|-<br />
|style="padding:.4em;"|2014-37<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://msb.embopress.org/content/10/9/752.long The role of the interactome in the maintenance of deleterious variability in human populations.]<br />
|-<br />
|style="padding:.4em;"|2014-36<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencemag.org/content/342/6154/1235587.long Integrative annotation of variants from 1092 humans: application to cancer genomics.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/12/02<br />
|style="padding:.4em;"|2014-35<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genome.cshlp.org/content/23/8/1319.long Mapping functional transcription factor networks from gene expression data.]<br />
|-<br />
|style="padding:.4em;"|2014-34<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nrg/journal/v15/n7/full/nrg3684.html In pursuit of design principles of regulatory sequences.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/25<br />
|style="padding:.4em;"|2014-33<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/3/6/36 Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease.]<br />
|-<br />
|style="padding:.4em;"|2014-32<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S009286741300891X Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/18<br />
|style="padding:.4em;"|2014-31<br />
|style="padding:.4em;"|SM Yang<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/6/8/64 The 'dnet' approach promotes emerging research on cancer patient survival.]<br />
|-<br />
|style="padding:.4em;"|2014-30<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414010368 Determination and inference of eukaryotic transcription factor sequence specificity.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/11/11<br />
|style="padding:.4em;"|2014-29<br />
|style="padding:.4em;"|DS Bae<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.pnas.org/content/110/16/6412.long Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles.]<br />
|-<br />
|style="padding:.4em;"|2014-28<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009350 Dissecting engineered cell types and enhancing cell fate conversion via CellNet.]<br />
|-<br />
|style="padding:.4em;"|2014-27<br />
|style="padding:.4em;"|HH Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009349 CellNet: network biology applied to stem cell engineering.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/11/04<br />
|style="padding:.4em;"|2014-26<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414009775 Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality.]<br />
|-<br />
|style="padding:.4em;"|2014-25<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3046.html Phen-Gen: combining phenotype and genotype to analyze rare disorders.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/10/28<br />
|style="padding:.4em;"|2014-24<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2877.html A community effort to assess and improve drug sensitivity prediction algorithms.]<br />
|-<br />
|style="padding:.4em;"|2014-23<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/ng/journal/v46/n9/full/ng.3051.html Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/30<br />
|style="padding:.4em;"|2014-22<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html Network-based stratification of tumor mutations.]<br />
|-<br />
|style="padding:.4em;"|2014-21<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.sciencedirect.com/science/article/pii/S0092867414001457 Synonymous mutations frequently act as driver mutations in human cancers.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/23<br />
|style="padding:.4em;"|2014-20<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003460 VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.]<br />
|-<br />
|style="padding:.4em;"|2014-19<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/13/12/R124 DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/16<br />
|style="padding:.4em;"|2014-18<br />
|style="padding:.4em;"|JH Shin<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomebiology.com/content/14/5/R52 Integrated analysis of recurrent properties of cancer genes to identify novel drivers.]<br />
|-<br />
|style="padding:.4em;"|2014-17<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://genomemedicine.com/content/4/11/89 Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/09/02<br />
|style="padding:.4em;"|2014-16<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23228031 A network module-based method for identifying cancer prognostic signatures.]<br />
|-<br />
|style="padding:.4em;"|2014-15<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24429628 Realizing the promise of cancer predisposition genes.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/19<br />
|style="padding:.4em;"|2014-14<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24952901 Assessing the clinical utility of cancer genomic and proteomic data across tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-13<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24132290 Mutational landscape and significance across 12 major cancer types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/12<br />
|style="padding:.4em;"|2014-12<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23945592 Signatures of mutational processes in human cancer.]<br />
|-<br />
|style="padding:.4em;"|2014-11<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24390350 Discovery and saturation analysis of cancer genes across 21 tumour types.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/08/05<br />
|style="padding:.4em;"|2014-10<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24084849 Comprehensive identification of mutational cancer driver genes across 12 tumor types.]<br />
|-<br />
|style="padding:.4em;"|2014-9<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24037244 IntOGen-mutations identifies cancer drivers across tumor types.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/29<br />
|style="padding:.4em;"|2014-8<br />
|style="padding:.4em;"|CY Kim<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23900255 Computational approaches to identify functional genetic variants in cancer genomes.]<br />
|-<br />
|style="padding:.4em;"|2014-7<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=23770567 Mutational heterogeneity in cancer and the search for new cancer-associated genes.]<br />
|-<br />
|style="padding:.4em;"|2014-6<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.nature.com/nmeth/journal/v11/n4/abs/nmeth.2891.html Cancer genomes: discerning drivers from passengers]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2014/07/22<br />
|style="padding:.4em;"|2014-5<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/24071849 The Cancer Genome Atlas Pan-Cancer analysis project.]<br />
|-<br />
|style="padding:.4em;"|2014-4<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/23539594 Cancer genome landscapes.]<br />
|-<br />
|style="padding:.4em;"|2014-3<br />
|style="padding:.4em;"|AR Cho<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=21900272 Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2014/07/15<br />
|style="padding:.4em;"|2014-2<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670764 A promoter-level mammalian expression atlas.]<br />
|-<br />
|style="padding:.4em;"|2014-1<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|<br />
[http://www.ncbi.nlm.nih.gov/pubmed/?term=24670763 An atlas of active enhancers across human cell types and tissues.]<br />
|}<br />
{|class=wikitable style="text-align:center;"<br />
|+style="text-align:left;font-size:12pt" | 2013<br />
|-<br />
!scope="col" style="padding:.4em" | Date<br />
!scope="col" style="padding:.4em" | Paper<br/>index<br />
!scope="col" style="padding:.4em" | Presenter<br />
!scope="col" style="padding:.4em" | Paper title<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/26<br />
|style="padding:.4em;"|2013-31<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://nar.oxfordjournals.org/content/40/16/7690.long Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages]<br />
|-<br />
|style="padding:.4em;"|2013-30<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n4/full/nbt.2519.html Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/06/04<br />
|style="padding:.4em;"|2013-29<br />
|style="padding:.4em;"|KS Kim<br />
|style="padding:.4em;text-align:left"|[https://www.cell.com/abstract/S0092-8674(13)00439-X Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding]<br />
|-<br />
|style="padding:.4em;"|2013-28<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/28<br />
|style="padding:.4em;"|2013-27<br />
|style="padding:.4em;"|YH Ko<br />
|style="padding:.4em;text-align:left"|[http://www.pnas.org/content/102/38/13544.long Discovering statistically significant pathways in expression profiling studies]<br />
|-<br />
|style="padding:.4em;"|2013-26<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058977 Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses]<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/21<br />
|style="padding:.4em;"|2013-25<br />
|style="padding:.4em;"|HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html Dynamic regulatory network controlling TH17 cell differentiation]<br />
|-<br />
|style="padding:.4em;"|2013-24<br />
|style="padding:.4em;"|T Lee<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412013529 Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/05/14<br />
|style="padding:.4em;"|2013-23<br />
|style="padding:.4em;"|JE Shim<br />
|style="padding:.4em;text-align:left"|[http://www.sciencedirect.com/science/article/pii/S0092867412015565 Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci]<br />
<br />
|-<br />
|style="padding:.4em;"|2013-22<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v45/n2/full/ng.2504.html Chromatin marks identify critical cell types for fine mapping complex trait variants]<br />
|-<br />
|style="padding:.4em;" rowspan=2|'''2013/05/07'''<br />
|style="padding:.4em;"|2013-21<br />
|style="padding:.4em;"|ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01555-3 Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues]<br />
|-<br />
|style="padding:.4em;"|2013-20<br />
|style="padding:.4em;"|HS Shim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003201 Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression]<br />
|-<br />
|style="padding:.4em;"|2013/04/09<br />
|style="padding:.4em;"|2013-19<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1790.long Annotation of functional variation in personal genomes using RegulomeDB]<br />
|-<br />
|style="padding:.4em;"|2013/04/02<br />
|style="padding:.4em;"|2013-18<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1775.long The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression]<br />
|-<br />
|style="padding:.4em;" |2013/03/12<br />
|style="padding:.4em;"|2013-17<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002311 Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/03/05<br />
|style="padding:.4em;"|2013-16<br />
|style="padding:.4em;"| ER Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nrg/journal/v10/n10/full/nrg2641.html ChIP–seq: advantages and challenges of a maturing technology]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/21<br />
|style="padding:.4em;"|2013-15<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002830 Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density]<br />
|-<br />
|style="padding:.4em;"|2013-14<br />
|style="padding:.4em;"| KS Kim<br />
|style="padding:.4em;text-align:left"|[http://www.cell.com/abstract/S0092-8674(12)01424-9 A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells]<br />
|-<br />
|style="padding:.4em;"|2013-13<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/6/1015.long Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/15<br />
|style="padding:.4em;"|2013-12<br />
|style="padding:.4em;"| HJ Han<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/ng/journal/v43/n3/full/ng.759.html Chromatin accessibility pre-determines glucocorticoid receptor binding patterns]<br />
|-<br />
|style="padding:.4em;"|2013-11<br />
|style="padding:.4em;"| JE Shim, CY Kim <br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2422.html Interpreting noncoding genetic variation in complex traits and human disease]<br />
|-<br />
|style="padding:.4em;"|2013-10<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/21/3/447.full.pdf+html Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/02/08<br />
|style="padding:.4em;"|2013-09<br />
|style="padding:.4em;"|HJ Kim<br />
|style="padding:.4em;text-align:left"|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002599 Widespread Site-Dependent Buffering of Human Regulatory Polymorphism]<br />
|-<br />
|style="padding:.4em;"|2013-08<br />
|style="padding:.4em;"|JE Shim, CY Kim<br />
|style="padding:.4em;text-align:left;"|[http://genome.cshlp.org/content/22/9/1748.long Linking disease associations with regulatory information in the human genome]<br />
|-<br />
|style="padding:.4em;"|2013-07<br />
|style="padding:.4em;"|HJ Han, JH Kim<br />
|style="padding:.4em;text-align:left"|[http://genome.cshlp.org/content/22/9/1658.long Understanding transcriptional regulation by integrative analysis of transcription factor binding data]<br />
|-<br />
|style="padding:.4em;" rowspan=3|2013/01/25<br />
|style="padding:.4em;"|2013-06<br />
|style="padding:.4em;"|HJ Han, '''JH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11279.html The long-range interaction landscape of gene promoters]<br />
|-<br />
|style="padding:.4em;"|2013-05<br />
|style="padding:.4em;"|'''ER Kim''', HS Shim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Landscape of transcription in human cells]<br />
|-<br />
|style="padding:.4em;"|2013-04<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html Architecture of the human regulatory network derived from ENCODE data]<br />
<br />
|-<br />
|style="padding:.4em;" rowspan=2|2013/01/18<br />
|style="padding:.4em;"|2013-03<br />
|style="padding:.4em;"|KS Kim, '''TH Kim'''<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html An expansive human regulatory lexicon encoded in transcription factor footprints]<br />
|-<br />
|style="padding:.4em;"|2013-02<br />
|style="padding:.4em;"|'''HJ Han''', JH Kim<br />
|style="padding:.4em;text-align:left;"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11232.html The accessible chromatin landscape of the human genome]<br />
|-<br />
|style="padding:.4em;" rowspan=1|2013/01/11<br />
|style="padding:.4em;"|2013-01<br />
|style="padding:.4em;"| '''JE Shim''', CY Kim<br />
|style="padding:.4em;text-align:left"|[http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html An integrated encyclopedia of DNA elements in the human genome]<br />
|}<br />
<br />
2012<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc; padding:5px;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper title<br />
|-<br />
|rowspan = "1"|2013/01/11<br />
|align ="center"|2012-81<br />
|[http://genome.cshlp.org/content/22/8/1589.full (TH Kim) MuSiC: identifying mutational significance in cancer genomes.]<br />
|-<br />
|rowspan = "1"|2012/12/04<br />
|align ="center"|2012-80<br />
|[http://genome.cshlp.org/content/22/8/1383 (CY KIM) Human genomic disease variants: A neutral evolutionary explanation]<br />
|-<br />
|rowspan = "2"|2012/11/20<br />
| align="center"|2012-79<br />
|[http://www.cell.com/abstract/S0092-8674(12)00639-3 (HS Shim) Circuitry and Dynamics of Human Transcription Factor Regulatory Networks]<br />
|-<br />
| align="center"|2012-78<br />
|[http://www.nature.com/nature/journal/v487/n7408/full/nature11288.html (HJ Kim) Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins]<br />
|-<br />
|rowspan = "2"|2012/11/06<br />
| align="center"|2012-77<br />
|[http://www.sciencemag.org/content/337/6099/1190.short (HJ Han) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA]<br />
|-<br />
| align="center"|2012-76<br />
|[http://www.pnas.org/cgi/doi/10.1073/pnas.1201904109 (KS Kim) A public resource facilitating clinical use of genomes] <br />
|-<br />
|rowspan = "6" |2012/07/19<br />
| align="center"|2012-75<br />
|[http://genome.cshlp.org/content/22/7/1334 (HJ Han & YH Ko) Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks]<br />
|-<br />
| align="center"|2012-74 <br />
|[http://www.sciencemag.org/content/337/6090/100.full (JE Shim) An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People] <br />
|-<br />
| align="center"|2012-73<br />
|[http://www.sciencemag.org/content/337/6090/64.abstract (JE Shim) Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes]<br />
|-<br />
| align="center"|2012-72<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063581/ (SH Hwang) Network-based classification of breast cancer metastasis]<br />
|-<br />
| align="center"|2012-71<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002707 (T Lee&CY Kim)Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants]<br />
|-<br />
| align="center"|2012-70<br />
|[http://genome.cshlp.org/content/20/9/1297 (ER Kim&TH Kim)The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data]<br />
|-<br />
|rowspan = "8" |2012/07/16<br />
| align="center"|2012-69<br />
|[http://www.nature.com/ng/journal/v43/n5/full/ng.806.html (ER Kim&TH Kim)A framework for variation discovery and genotyping using next-generation DNA sequencing data]<br />
|-<br />
| align="center"|2012-66<br />
|[http://bioinformatics.oxfordjournals.org/content/25/16/2078.long (ER Kim&TH Kim)The Sequence Alignment/Map format and SAMtools]<br />
|-<br />
| align="center"|2012-65<br />
|[http://bioinformatics.oxfordjournals.org/content/early/2011/06/07/bioinformatics.btr330 (ER Kim&TH Kim)The Variant Call Format and VCFtools]<br />
|-<br />
| align="center"|2012-64<br />
|[http://www.cell.com/abstract/S0092-8674(12)00104-3 (YH Go&HJ Han)The Impact of the Gut Microbiota on Human Health: An Integrative View]<br />
|-<br />
|align="center"|2012-63<br />
|[http://www.sciencemag.org/content/336/6086/1262.abstract (T Lee&CY Kim)Host-Gut Microbiota Metabolic Interactions]<br />
|-<br />
|align="center"|2012-62<br />
|[http://www.sciencemag.org/content/336/6086/1268.full (AR Cho,JH Ju)Interactions Between the Microbiota and the Immune System]<br />
|-<br />
|align="center"|2012-61<br />
|[http://www.sciencemag.org/content/336/6086/1255.abstract (SH Hwang&HJ Cho)The Application of Ecological Theory Toward an Understanding of the Human Microbiome]<br />
|-<br />
|align="center"|2012-60<br />
|[http://stm.sciencemag.org/content/4/137/137rv5 (SH Hwang&HJ Cho)Microbiota-Targeted Therapies: An Ecological Perspective]<br />
|-<br />
|rowspan = "3" |2012/07/13<br />
|align="center"|2012-59<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002358 (JH Shin&HJ Kim)Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome]<br />
|-<br />
| align="center"|2012-58<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html (JH Shin&HJ Kim)A framework for human microbiome research]<br />
|-<br />
|align="center"|2012-57<br />
|[http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html (JH Shin&HJ Kim)Structure, function and diversity of the healthy human microbiome]<br />
|-<br />
|rowspan = "4" |2012/07/12<br />
|align="center"|2012-56<br />
|[http://nar.oxfordjournals.org/content/40/D1/D957.long (AR Cho&JH Ju)COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines]<br />
|-<br />
|align="center"|2012-55<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002511 (YH Go&HJ Han)Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes]<br />
|-<br />
| align="center"|2012-54<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201147.html (YH Go&HJ Han)A pharmacogenomic method for individualized prediction of drug sensitivity]<br />
|-<br />
|align="center"|2012-53<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10983.html (JH Soh)The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups]<br />
|-<br />
|rowspan = "6" |2012/07/09<br />
|align="center"|2012-52<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11003.html (ER Kim&TH Kim)The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity]<br />
|-<br />
|align="center"|2012-51<br />
|[http://www.nature.com/nature/journal/v483/n7391/full/nature11005.html (ER Kim&TH Kim)Systematic identification of genomic markers of drug sensitivity in cancer cells]<br />
|-<br />
| align="center"|2012-50<br />
|[http://www.pnas.org/content/early/2011/10/13/1018854108.abstract (ER Kim&TH Kim)Subtype and pathway specific responses to anticancer compounds in breast cancer]<br />
|-<br />
|align="center"|2012-49<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10945.html (JE Shim&KS Kim)De novo mutations revealed by whole-exome sequencing are strongly associated with autism]<br />
|-<br />
|align="center"|2012-48<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11011.html (JE Shim&KS Kim)Patterns and rates of exonic de novo mutations in autism spectrum disorders]<br />
|-<br />
|align="center"|2012-47<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10989.html (JE Shim&KS Kim)Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations]<br />
|-<br />
|rowspan = "6" |2012/07/06<br />
| align="center"|2012-46<br />
|[http://www.g3journal.org/content/1/3/233.full (T Lee&CY Kim)Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)]<br />
|-<br />
|align="center"|2012-45<br />
|[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002621 (T Lee&CY Kim)Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases]<br />
|-<br />
|align="center"|2012-44<br />
|[http://www.nature.com/nature/journal/v480/n7376/full/nature10665.html (AR Cho&JH Ju)Predicting mutation outcome from early stochastic variation in genetic interaction partners]<br />
|-<br />
|align="center"|2012-43<br />
|[http://www.sciencemag.org/content/335/6064/82 (AR Cho&JH Ju)Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans]<br />
|-<br />
| align="center"|2012-42<br />
|[http://genome.cshlp.org/content/22/6/1163 (JE Shim&KS Kim)Identification of microRNA-regulated gene networks by expression analysis of target genes]<br />
|-<br />
|align="center"|2012-41<br />
|[http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html (JE Shim&KS Kim)Exome sequencing and the genetic basis of complex traits]<br />
|-<br />
|rowspan = "6" |2012/07/02<br />
|align="center"|2012-40<br />
|[http://www.cell.com/abstract/S0092-8674(12)00573-9 (JH Soh)Functional Repurposing Revealed by Comparing S. pombe and S. cerevisiae Genetic Interactions]<br />
|-<br />
|align="center"|2012-39<br />
|[http://genome.cshlp.org/content/22/2/375.long (ER Kim&TH Kim)De novo discovery of mutated driver pathways in cancer]<br />
|-<br />
| align="center"|2012-38<br />
|[http://www.nature.com/msb/journal/v4/n1/full/msb20082.html (YH Go&HJ Han)A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas]<br />
|-<br />
|align="center"|2012-37<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201126.html (SH Hwang&HJ Cho)PREDICT: a method for inferring novel drug indications with application to personalized medicine]<br />
|-<br />
|align="center"|2012-36<br />
|[http://www.nature.com/nature/journal/v453/n7198/full/nature06973.html (SH Hwang&HJ Cho)Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype]<br />
|-<br />
|align="center"|2012-35<br />
|[http://www.sciencemag.org/content/334/6062/1518.full (JH Shin&HJ Kim)Detecting Novel Associations in Large Data Sets]<br />
|-<br />
|rowspan = "3" |2012/03/05<br />
| align="center"|2012-34<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|align="center"|2012-33<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|align="center"|2012-32<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |2012/02/27<br />2012/02/28<br />
| align="center"|2012-31<br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|align="center"|2012-30<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|align="center"|2012-29<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|align="center"|2012-28<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|align="center"|2012-27<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|align="center"|2012-26<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|align="center"|2012-25<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |2012/02/06<br />
| align="center"|2012-24<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|align="center"|2012-23<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|align="center"|2012-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|align="center"|2012-21<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|align="center"|2012-20<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |2012/01/30<br />
|align="center"|2012-19<br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|align="center"|2012-18<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|align="center"|2012-17<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|align="center"|2012-16<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|align="center"|2012-15<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />
|align="center"|2012-14<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|align="center"|2012-13<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|align="center"|2012-12<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |2012/01/09<br />2012/01/16<br />
| align="center"|2012-11<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|align="center"|2012-10<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|align="center"|2012-09<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|align="center"|2012-08<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|align="center"|2012-07<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|align="center"|2012-06<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-05<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|align="center"|2012-04<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|align="center"|2012-03<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |2012/01/09<br />2012/01/16<br />
|align="center"|2012-02<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|align="center"|2012-01<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|}<br />
2011<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "6" |2011/11/28<br />
|align="center"|2011-49<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|align="center"|2011-48<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|align="center"|2011-47<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|align="center"|2011-46<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|align="center"|2011-45<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|align="center"|2011-44<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" |2011/11/14<br />
|align="center"|2011-43<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|align="center"|2011-42<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|align="center"|2011-41<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" |2011/11/07<br />
|align="center"|2011-40<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|align="center"|2011-39<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|align="center"|2011-38<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|align="center"|2011-37<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" |2011/11/07 <br />
|align="center"|2011-36<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|align="center"|2011-35<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|align="center"|2011-34<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" |2011/10/05<br />
|align="center"|2011-33<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|align="center"|2011-32<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|align="center"|2011-31<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |2011/10/04<br />
|align="center"|2011-30<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|align="center"|2011-29<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|align="center"|2011-28<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|align="center"|2011-27<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |2011/09/19<br />
|align="center"|2011-26<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|align="center"|2011-25<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" |2011/09/05<br />
|align="center"|2011-24<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|align="center"|2011-23<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" |2011/09/22 <br />
|align="center"|2011-22<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|align="center"|2011-21<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|2011/06/20<br />
|align="center"|2011-20<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |2011/03/30<br />
|align="center"|2011-19<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|align="center"|2011-18<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
|rowspan = "2" |2011/03/16<br />
|align="center"|2011-17<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|align="center"|2011-16<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |2011/04/25<br />
|align="center"|2011-15<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|align="center"|2011-14<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|align="center"|2011-13<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |2011/04/11<br />
|align="center"|2011-12<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|align="center"|2011-11<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|2011/03/28<br />
|align="center"|2011-10<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|align="center"|2011-09<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|2011/03/14<br />
|align="center"|2011-08<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|align="center"|2011-07<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
|rowspan = "2"|2011/02/28<br />
|align="center"|2011-06<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|align="center"|2011-05<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|2011/02/21<br />
|align="center"|2011-04<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|2011/02/14<br />
|align="center"|2011-03<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|2011/01/31<br />
|align="center"|2011-02<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|align="center"|2011-01<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|}<br />
2010<br />
{|border ="1"<br />
|style="color:black; background-color:#dcdcdc;" align="center" |Date<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_index<br />
|style="color:black; background-color:#dcdcdc;" align="center"|Paper_title<br />
|-<br />
|rowspan = "2"|2010/12/27<br />
|align="center"|2010-29<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|align="center"|2010-28<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|2010/11/15<br />
|align="center"|2010-27<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|align="center"|2010-26<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|2010/11/01<br />
|align="center"|2010-25<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|align="center"|2010-24<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|2010/10/11<br />
|align="center"|2010-23<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|rowspan = "2"|2010/09/13<br />
|align="center"|2010-22<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
|-<br />
|align="center"|2010-21<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|2010/05/26<br />
|align="center"|2010-20<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|2010/05/19<br />
|align="center"|2010-19<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|2010/04/21<br />
|align="center"|2010-18<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|2010/04/14<br />
|align="center"|2010-17<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |2010/04/07<br />
|align="center"|2010-16<br />
|[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|align="center"|2010-15<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|rowspan="2"|2010/03/31<br />
|align="center"|2010-14<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
|-<br />
|align="center"|2010-13<br />
|[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|2010/03/24<br />
|align="center"|2010-12<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|2010/01/18<br />
|align="center"|2010-11<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|2010/01/16<br />
|align="center"|2010-10<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|2010/01/15<br />
|align="center"|2010-09<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|2010/01/14<br />
|align="center"|2010-08<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|2010/01/13<br />
|align="center"|2010-07<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|2010/01/12<br />
|align="center"|2010-06<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|2010/01/11<br />
|align="center"|2010-05<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|2010/01/09<br />
|align="center"|2010-04<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|2010/01/08<br />
|align="center"|2010-03<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|2010/01/07<br />
|align="center"|2010-02<br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|2010/01/06<br />
|align="center"|2010-01<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
<br />
<br />
<br />
<br />
<!--<br />
{| border ="1"<br />
{| border ="1"<br />
|rowspan = "3" |<br />
|rowspan = "3" |March 5 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18516045 (8,HH Kim)Mapping and quantifying mammalian transcriptomes by RNA-Seq.]<br />
|-<br />
|[http://genomebiology.com/2010/11/10/R106 (11,Go&Ju)Differential expression analysis for sequence count data]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/26/1/139.short (12,Go&Ju)edgeR: a Bioconductor package for differential expression analysis of digital gene expression data ]<br />
|-<br />
|rowspan = "7" |***<br />
|rowspan = "7" |February 27 Mon~28 Tue, 2012<br />
|rowspan = "7" | <br />
|[http://www.nature.com/nrg/journal/v10/n1/full/nrg2484.html (1,JW Song)RNA-Seq: a revolutionary tool for transcriptomics]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1613.html (2,JW Song)Computational methods for transcriptome annotation and quantification using RNA-seq]<br />
|-<br />
|[http://genomebiology.com/2010/11/12/220 (3,HJ Han)From RNA-seq reads to differential expression results]<br />
|-<br />
|[http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html (4,AR Cho)Comprehensive comparative analysis of strand-specific RNA sequencing methods]<br />
|-<br />
|[http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0026426 (5,T Lee)A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq]<br />
|-<br />
|[http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html (6,So&Shin)Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation]<br />
|-<br />
|[http://bioinformatics.oxfordjournals.org/content/25/9/1105.abstract (7,So&Shin)TopHat: discovering splice junctions with RNA-Seq]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |February 6 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125733/ mirConnX: condition-specific mRNA-microRNA network integrator]<br />
|-<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002190 Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data]<br />
|-<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002415 A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures]<br />
|-<br />
|[http://genome.cshlp.org/content/20/5/589.short Reprogramming of miRNA networks in cancer and leukemia]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)01152-4 An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma]<br />
|-<br />
|rowspan = "5" |<br />
|rowspan = "5" |January 30 Mon, 2012<br />
|rowspan = "5" | <br />
|[http://www.cell.com/abstract/S0092-8674(11)00237-6 Principles and Strategies for Developing Network Models in Cancer]<br />
|-<br />
|[http://www.nature.com/ng/journal/v37/n4/full/ng1532.html Reverse engineering of regulatory networks in human B cells]<br />
|-<br />
|[http://www.nature.com/nature/journal/v452/n7186/abs/nature06757.html Variations in DNA elucidate molecular networks that cause disease]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779083/ Harnessing gene expression to identify the genetic basis of drug resistance]<br />
|-<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867410012936 An Integrated Approach to Uncover Drivers of Cancer]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18704161 Genetic variation in an individual human exome.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/22081227 Predicting phenotypic variation in yeast from individual genome sequences.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical assessment incorporating a personal genome.]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "6" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20399638 Human allelic variation: perspective from protein function, structure, and evolution.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19561590 Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11230178 Prediction of deleterious human alleles.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12202775 Human non-synonymous SNPs: server and survey.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/20354512 A method and server for predicting damaging missense mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920242/ SNAP: predict effect of non-synonymous polymorphisms on function]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "3" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21920052 Computational and statistical approaches to analyzing variants identified by exome sequencing.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18179889 Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19684571 Targeted capture and massively parallel sequencing of 12 human exomes.]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |January 9 Mon, 2012<br>January 16 Mon, 2012<br />
|rowspan = "2" | <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17637733 The distribution of fitness effects of new mutations.]<br />
|-<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724/ Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies]<br />
|-<br />
|rowspan = "6" |<br />
|rowspan = "6" |November 28 Mon, 2011<br />
|rowspan = "6" | TY Oh, <br><br />
SH Hwang, <br><br />
JE Shim, <br><br />
S Beck, <br><br />
JH Shin<br />
|[http://bmir.stanford.edu/file_asset/index.php/1407/BMIR-2009-1355.pdf (Shin)Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v4/n11/abs/nchembio.118.html (Shin)Network pharmacology: the next paradigm in drug discovery]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201171.html (Oh)Systematic exploration of synergistic drug pairs]<br />
|-<br />
|[http://www.nature.com/msb/journal/v5/n1/full/msb200995.html (Shim)Chemogenomic profiling predicts antifungal synergies]<br />
|-<br />
|[http://www.pnas.org/content/104/32/13086 (Beck)A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery]<br />
|-<br />
|[http://www.nature.com/nchembio/journal/v1/n7/full/nchembio747.html (Hwang)Analysis of drug-induced effect patterns to link structure and side effects of medicines]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 14 Mon, 2011<br />
|rowspan = "3" | HH Kim & AR Cho<br />
|[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000662 Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb201131.html Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20115.html Analysis of multiple compound–protein interactions reveals novel bioactive molecules]<br />
|-<br />
|rowspan = "4" | <br />
|rowspan = "4" |November 7 Mon, 2011<br />
|rowspan = "4" | YH Ko<br />
|[http://www.nature.com/nbt/journal/v25/n10/abs/nbt1338.html Drug—target network]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb200998.html A side effect resource to capture phenotypic effects of drugs]<br />
|-<br />
|[http://genome.cshlp.org/content/18/2/206.long Quantitative systems-level determinants of human genes targeted by successful drugs]<br />
|-<br />
|[http://www.sciencemag.org/content/321/5886/263.short Drug Target Identification Using Side-Effect Similarity]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |November 7 Mon, 2011<br />
|rowspan = "3" | JW Song<br />
|[http://stm.sciencemag.org/content/3/96/96ra77.short Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data]<br />
|-<br />
|[http://bib.oxfordjournals.org/content/12/4/303.short Exploiting drug–disease relationships for computational drug repositioning]<br />
|-<br />
|[http://www.springerlink.com/content/4489r051nu2t0ul1/ Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks]<br />
|-<br />
|rowspan = "3" | <br />
|rowspan = "3" |October 5 Mon, 2011<br />
|rowspan = "3" | HH Kim<br />
|[http://genome.cshlp.org/content/20/7/960.full Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families]<br />
|-<br />
|[http://www.pnas.org/content/106/5/1374.full Quantifying environmental adaptation of metabolic pathways in metagenomics]<br />
|-<br />
|[http://www.pnas.org/content/104/35/13913.abstract Quantitative assessment of protein function prediction from metagenomics shotgun sequences]<br />
|-<br />
|rowspan = "4" |<br />
|rowspan = "4" |October 4 Mon, 2011<br />
|rowspan = "4" | S Beck<br />
|[http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html A human gut microbial gene catalogue established by metagenomic sequencing]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function]<br />
|-<br />
|[http://genome.cshlp.org/content/early/2009/04/20/gr.085464.108 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges]<br />
|-<br />
|[http://www.nature.com/nrmicro/journal/v9/n4/full/nrmicro2540.html Unravelling the effects of the environment and host genotype on the gut microbiome]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |September 19 Mon, 2011<br />
|rowspan = "2" | TY Oh<br />
|[http://www.sciencemag.org/content/333/6042/596.full independently evolved virulence effectors converge onto hubs in a plant immune system Network]<br />
|-<br />
|[http://www.sciencemag.org/content/333/6042/601.full Evidence for network evolution in an arabidopsis interactome Map]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" |September 5 Mon, 2011<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science/article/pii/S0092867411005861 Exome Sequencing of Ion Channel Genes Reveals Complex Profiles Confounding Personal Risk Assessment in Epilepsy]<br />
|-<br />
|SH Hwang<br />
|[http://www.cell.com/abstract/S0092-8674(11)00543-5 Pluripotency factors in Embryonic stem cells Regulate Differentiation into Germ Layers]<br />
|-<br />
|rowspan = "2" | <br />
|rowspan = "2" | August 22 Mon, 2011<br />
|ER Kim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002077 Integrated Genome-scale predition of Detrimental Mutations in Transcription Networks]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/nrg/journal/v12/n4/abs/nrg2969.html From expression QTLs to personalized transcriptomics]<br />
|-<br />
|<br />
|June 20 Mon, 2011<br />
|JH Shin<br />
|[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001046 a user's guide to the encyclopedia of DNA elements(ENCODE)]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 30 Mon, 2011<br />
|rowspan = "2" | HH Kim<br />
|[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09944.html enterotypes of the human gut microbiome]<br />
|-<br />
|[http://www.nature.com/msb/journal/v7/n1/full/msb20116.html toward molecular trait-based ecology, through intergration of biogeochemical, geographical and metagenomic data]<br />
|-<br />
<br />
|rowspan = "2" |<br />
|rowspan = "2" | May 16 Mon, 2011<br />
|rowspan = "2" | AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002047 variable pathogenicity determines individual lifespan in ''caenorhabditis elegans'']<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00371-0 a high-resolution ''c.elegans'' essential gene network based on phenotypic profiling of a complex tissue]<br />
|-<br />
|rowspan = "3" |<br />
|rowspan = "3" |April 25 Mon, 2011<br />
|rowspan = "3" |S Beck<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/21376230 Hallmarks of Cancer : The next generation]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00296-0 Mapping Cancer Origins]<br />
|-<br />
|[http://www.cell.com/abstract/S0092-8674(11)00297-2 Genetic Interactions in Cancer Progression and Treatment]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 11 Mon, 2011<br />
|JE Shim<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001273 Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology]<br />
|-<br />
|T Lee<br />
|***Changed!***<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19557189 Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 28 Mon, 2011<br />
|rowspan = "2"|TY Oh<br />
|[http://www.pnas.org/content/106/44/18843.long profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201076.html cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|March 14 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-51SFHJD-1&_user=44062&_coverDate=01%2F07%2F2011&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=2f6017aab4c794ed7e78fbbd8447077a&searchtype=a phenotypic landscape of a bacterial cell]<br />
|-<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb2010107.html cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action]<br />
|-<br />
<br />
|rowspan = "2"|<br />
|rowspan = "2"|February 28 Mon, 2011<br />
|KS Kim<br />
|[http://www.pnas.org/content/early/2010/09/23/1004666107.abstract genomic patterns of pleiotropy and the evolution of complexity]<br />
|-<br />
|HJ Han<br />
|[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001009 simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway]<br />
|-<br />
|<br />
|February 21 Mon, 2011<br />
|MH Lee<br />
|[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html dynamic interaction networks in a hierarchically organized tissue]<br />
|-<br />
|<br />
|February 14 Mon, 2011<br />
|AR Cho<br />
|[http://www.sciencemag.org/content/330/6009/1385.abstract rewiring of genetic networks in response to DNA damage]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|January 31 Mon, 2011<br />
|rowspan = "2"|JW Song<br />
|[http://www.nature.com/nrg/journal/v10/n9/abs/nrg2633.html Applying mass spectrometry-based proteomics to genetics, genomics and network biology]<br />
|-<br />
|[http://physiolgenomics.physiology.org/content/33/1/18.long Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2" | December 27 Mon, 2010<br />
|ER Kim<br />
|[http://www.nature.com/nature/journal/v467/n7312/full/nature09326.html Functional_roles_fornoise_in_genetic_circuits]<br />
|-<br />
|T Lee<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.610.html Estimation_of_effect_size_distribution_from_genome-wide_association_studies_and_implications_for_future_discoveries]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 15 Mon, 2010<br />
|AR Cho<br />
|[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000932 Liver_and_Adipose_Expression_associated_SNPs_are_enriched_for_association_to_type_2_diabetes]<br />
|-<br />
|SG Ji<br />
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDC-50J4MRJ-2&_user=44062&_coverDate=10%2F10%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000004738&_version=1&_urlVersion=0&_userid=44062&md5=7667a67cf8ba3f68117b8d0ff85a8887&searchtype=a It's_the_machine_that_matters:_predicting_gene_function_and_phenotype_from_protein_networks]<br />
|-<br />
|rowspan = "2"|<br />
|rowspan = "2"|November 1 Mon, 2010<br />
|HH Kim<br />
|[http://genome.cshlp.org/content/early/2010/06/15/gr.104216.109 A_genome-wide_map_of_human_genetic_interactions_inferred_from_radiation_hybrid_genotypes]<br />
|-<br />
|JH Shin<br />
|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012139 A_Genome-Wide_Gene_Function_Prediction_Resource_for_Drosophila_melanogaster]<br />
|-<br />
|<br />
|October 11 Mon, 2010<br />
|JE Shim<br />
|[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913399/?tool=pubmed Dissecting_spatio-temporal_protein_networks_driving_human_heart_development_and_related_disorders]<br />
|-<br />
|<br />
|September 13 Mon, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/ng/journal/v42/n7/full/ng.600.html Transposable_elements_have_rewired_the_core_regulatory_network_of_human_embryonic_stem_cells]<br />
[http://www.nature.com/ng/journal/v42/n7/full/ng0710-557.html Limits_of_sequence_and_functional_conservation]<br />
|-<br />
|<br />
|May 26 Wed, 2010<br />
|AR Cho<br />
|[[media:100428_network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf|network_based_elucidation_of_human_disease_similarities_reveals_common_functional_modules_enriched_for_pluripotent_drug_targets.pdf]]<br />
|-<br />
|<br />
|May 19 Wed, 2010<br />
|SG Ji<br />
|[[media:100421_interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf|interpreting_metabolomic_profiles_using_unbiased_pathway_models.pdf]]<br />
|-<br />
|<br />
|April 21 Wed, 2010<br />
|JH Shin<br />
|[[media:100414_identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf|identification_of_networks_of_co_occurring_tumor_related_dna_copy_number_changes_using_a_genome_wide_scoringapproach.pdf]]<br />
|-<br />
|<br />
|April 14 Wed, 2010<br />
|TY Oh<br />
|[http://www.cell.com/retrieve/pii/S0092867410000796 an_atlas_of_combinatorial_transcriptional_regulation_in_mouse_and_man]<br />
|-<br />
|rowspan = "2" |<br />
|rowspan = "2" |April 7 Wed, 2010<br />
|HHkim<br />
|<br />
[http://www.pnas.org/content/early/2010/03/11/0910200107.long systematic_discovery_of_nonobvious_human_disease_models_through_orthologous_phenotypes]<br />
|-<br />
|T Lee<br />
|<br />
[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08800.html genome_side_association_study_of_107_phenotypes_in_Arabidopsis_thaliana_inbred_lines]<br />
|-<br />
|<br />
|Mar 31 Wed, 2010<br />
|JE Shim<br />
|[[media:100331_toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf|toward_stem_cell_systems_biology_from_molecules_to_networks_and_landscapes.pdf]]<br />
[http://www.nature.com/nrm/journal/v10/n10/abs/nrm2766.html systems_biology_of_stem_cell_fate_and_cellular_reprogramming]<br />
|-<br />
|<br />
|Mar 24 Wed, 2010<br />
|SH Hwang<br />
|[http://www.nature.com/nbt/journal/v27/n2/abs/nbt.1522.html dynamic_modularity_in_protein_interaction_networks_predicts_breast_cancer_outcome]<br />
|-<br />
|<br />
|Jan 18 Mon, 2010<br />
|TY Oh(T Lee)<br />
|JournalClub_100118_a_tutorial_on_statistical_methods_for_population_association_studies<br />
|-<br />
|<br />
|Jan 16 Sat, 2010<br />
|JE Shim(MH Lee)<br />
|systems-level_dinamic_analyses_of_fate_change_in_murine_embryonic_stem_cells<br />
|-<br />
|<br />
|Jan 15 Fri, 2010<br />
|SG Ji<br />
|distinguishing_direct_versus_indirect_transcription_factor-DNA-interactions<br />
|-<br />
|<br />
|Jan 14 Thu, 2010<br />
|HH kim<br />
|chemogenomic_profiling_predicts_antifungal_synergies<br />
|-<br />
|<br />
|Jan 13 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|edgetic_perturbation_models_of_human_inherited_disorders<br />
|-<br />
|<br />
|Jan 12 Tue, 2010<br />
|TY Oh(T Lee)<br />
|analysis_of_cell_fate_from_single-cell_gene_expression_profiles_in_C.elegans<br />
|-<br />
|<br />
|Jan 11 Mon, 2010<br />
|JE Shim(MH Lee)<br />
|predicting_new_molecular_targets_for_known_drugs.pdf<br />
Reference:SEA(Similarity Ensemble Approach)<br />
|-<br />
|<br />
|Jan 09 Sat, 2010<br />
|SG Ji<br />
|harnessing_gene_expression_to_identify_the_genetic_basis_of_drug_resistance<br />
|-<br />
|<br />
|Jan 08 Fri, 2010<br />
|AR Cho<br />
|an_integrative_approach_to_reveal_driver_gene_fusions_from_paired_end_sequencing_data_in_cancer<br />
|-<br />
|<br />
|Jan 07 Thu, 2010<br />
|HH Kim <br />
|a_phenotypic_profile_of_the_candida_albicans_regulatory_network<br />
|-<br />
|<br />
|Jan 06 Wed, 2010<br />
|JH Shin(ER Kim)<br />
|a_global_view_of_protein_expression_in_human_cells_tissues_and_organs<br />
|}<br />
--></div>
Administrator
https://netbiolab.org/w/Research
Research
2016-04-06T14:18:28Z
<p>Administrator: </p>
<hr />
<div>=='''Research Summary'''==<br />
<div style="float:right;margin:5px 40px;">{{#widget:AddHtml|content=<img src="../wiki/cloud.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div><br />
<div style="text-align:justify;"><br />
The ultimate goal of biological research is to manipulate traits that are important for medicine, agriculture, and bio-industry. This challenging task first requires good understanding of association between genotype and phenotype. Because of high complexity of genotype as well as phenotype, complexity of the genotype-phenotype association could be even untouchable by combinatorial explosion of the number of possible associations. Therefore, modern genetics needs to be more systematic and predictive. Recently we proposed network-guided approach for genetics of complex traits. First, we construct probabilistic functional gene networks for cells or organisms by benchmarking and integrating heterogeneous multi-omics data that are in general publicly available. Then, using guilt-by-association, and other algorithms of network propagation of known biological information, we predict gene functions, phenotypic effect of loss-of-function, and epistatic interaction. The information can contribute to reconstruction of map between genotype and phenotype. The network-guided genetics method has been effectively applied for various organisms; from simple microbe yeast, to multicellular animal C. elegans, to the reference plant Arabidopsis, to the reference crop rice, and to the human.</div><br />
<br />
=='''Research Highlight'''==<br />
*[[media:research_highlight_004.pdf|2011 Nature Reviews Genetics, Research highlight (Predicting genetic interaction)]]<br />
*[[media:research_highlight_002.pdf|2008 Bioessay, What the papers say (WormNet)]]<br />
*[[media:research_highlight_003.pdf|2008 Genome Biology, Minireview (WormNet)]]<br />
*[[media:research_highlight_001.pdf|2008 Nature methods, Research highlight (WormNet)]]<br />
*[[media:Gallery_NGcover_SmallVer.jpg|2008 Nature Genetics coverstory (WormNet): Network perturbation predicts phenotype]]</div>
Administrator
https://netbiolab.org/w/Welcome_to_Network_Biology_Laboratory
Welcome to Network Biology Laboratory
2016-04-06T14:17:50Z
<p>Administrator: </p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
|rowspan="2" style="padding-right:20px;"|<br />
[[File :Groupphoto_20150601_5.jpeg|580px|center|middle|Main Photo]]<br />
<br />
|colspan=2|<br />
=== Research Keyword Cloud ===<br />
<div>{{#widget:AddHtml|content=<img src="../wiki/cloud.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div><br />
|-<br />
|<br />
=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| JE Shim*<br />
|style="width:65px"| T Lee<br />
|style="width:65px"| HJ Han<br />
|-<br />
| KS Kim<br />
| ER Kim<br />
| CY Kim<br />
|-<br />
| DS Bae<br />
| SM Yang<br />
| MY Lee<br />
|}<br />
|<br />
<br />
=== Visitors Trend ===<br />
[http://www2.clustrmaps.com/user/563d3fa7 http://www2.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]<br />
|-<br />
|colspan=3|<br />
===Contact Informations===<br />
<pre><br />
Yonsei University 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea <br />
Office: Engineering Research Park B118DA<br />
+82-70-8625-5205 <br />
</pre><br />
|}</div>
Administrator
https://netbiolab.org/w/Welcome_to_Network_Biology_Laboratory
Welcome to Network Biology Laboratory
2016-03-18T10:29:05Z
<p>Administrator: </p>
<hr />
<div>__NOTOC__<br />
<br />
{|border = "0" valign="top"<br />
|rowspan="2" style="padding-right:20px;"|<br />
[[File :Groupphoto_20150601_5.jpeg|580px|center|middle|Main Photo]]<br />
<br />
|colspan=2|<br />
=== Research Keyword Cloud ===<br />
<div>{{#widget:AddHtml|content=<img src="../cloud.jpg" alt="Word Cloud from Abstraction below publications" title="Word Cloud of NBL Publications' Abstract" />}}</div><br />
|-<br />
|<br />
=== Oral Presentation ===<br />
{|class=wikitable style="text-align:center;"<br />
|-<br />
|style="width:65px"| JE Shim*<br />
|style="width:65px"| T Lee<br />
|style="width:65px"| HJ Han<br />
|-<br />
| KS Kim<br />
| ER Kim<br />
| CY Kim<br />
|-<br />
| DS Bae<br />
| SM Yang<br />
| MY Lee<br />
|}<br />
|<br />
<br />
=== Visitors Trend ===<br />
[http://www2.clustrmaps.com/user/563d3fa7 http://www2.clustrmaps.com/stats/maps-no_clusters/www.netbiolab.org-thumb.jpg]<br />
|-<br />
|colspan=3|<br />
===Contact Informations===<br />
<pre><br />
Yonsei University 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea <br />
Office: Engineering Research Park B118DA<br />
+82-70-8625-5205 <br />
</pre><br />
|}</div>
Administrator
https://netbiolab.org/w/WMI
WMI
2016-03-18T09:06:28Z
<p>Administrator: Redirected page to Domain-based PPI network by Weighted Mutual Information (WMI)</p>
<hr />
<div>#REDIRECT [[Domain-based PPI network by Weighted Mutual Information (WMI)]]</div>
Administrator
https://netbiolab.org/w/Software
Software
2016-01-05T01:12:31Z
<p>Administrator: </p>
<hr />
<div>__NOTOC__<br />
=='''Co-functional networks: Organism-specific network-assisted hypothesis generation servers'''==<br />
<br />
==''Animal''==<br />
{|border="0" width="800"<br />
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]<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"|''Mus musculus''<br />
|align="center"|''Caenorhabditis elegans''<br />
|align="center"|''Drosophila melanogaster''<br />
|align="center"|''Homo sapiens''<br />
|}<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 />
<br />
=='''RIDDLE: Network-assisted Gene Set Analysis (human only)'''==<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 />
<br />
<br />
=='''MORPHIN: Network-assisted prediction of disease pathways in model organisms'''==<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 />
<br />
<br />
=='''JiffyNet:Instant gene network building server for newly sequenced species'''==<br />
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]] Jiffy (instant) gene network modeler for newly sequenced species<br />
<br />
<br />
=='''TRRUST: A reference database of human TF-target interactions'''==<br />
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] TRRUST (Transcriptional Regulatory relationships Unraveled by Sentence-based Text mining) is currently available for only human genes.</div>
Administrator
https://netbiolab.org/w/MediaWiki:Sidebar
MediaWiki:Sidebar
2016-01-05T01:11:42Z
<p>Administrator: </p>
<hr />
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