Network Biology Lab - User contributions [en]

Publications

2026-04-15T12:30:09Z

Il1001: /* 2026 (8) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (8)==
*134. Metformin beyond Glycemic Control: New Mechanistic Insights and Expanding Therapeutic Horizons, '''''Under Review'''''
 
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Under Review'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Revision'''''
 
*131. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*130. Yura Seo*, Yoon Dae Han, Linda Bojmar, Kyung-A Kim, Yurin Seo, Taeyul K. Kim, Suho Lee, Yeleem Kim, Hye Bin Choi, Yujin H. Lim, Chae Hyun Kim, Alexander Sandberg, Chuanwen Fan, Pernille Lauritzen, Henrik Molina, Christopher Peralta, Jacob B. Geri, Colin Burdette, Dai Hoon Han, Heon Yung Gee, '''Insuk Lee''', Jeon-Soo Shin, Hyunwook Kim, Leon Li, Gabriel C. Tobias, Inbal Wortzel, Sang Joon Shin, Hyo-Il Jung, Min Goo Lee, Soonmyung Paik, Robert E. Schwartz, Joong Bae Ahn, David Lyden, Han Sang Kim**, Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Journal of Extracellular Vesicles''''' 2026 Apr;15(4):e70278 [https://pubmed.ncbi.nlm.nih.gov/41979056/ pubmed]
 
*129. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Nature Communications''''' 2026 Apr 14;17(1):3467 [https://pubmed.ncbi.nlm.nih.gov/41980943/ pubmed]
 
*128. '''Jun Hyung Cha*, Sol-Ah Jeong*''', Byoung-Seok Ye, '''Insuk Lee**, Bock-Young Jung**''', Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia, '''''Journal of Oral Microbiology''''' 2026 Mar 11;18(1):2643036 [https://pubmed.ncbi.nlm.nih.gov/41836788/ pubmed]
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [//pubmed.gov/36289209 PubMed] [//www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [//pubmed.gov/36291657 PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [//pubmed.gov/36057640 PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [//pubmed.gov/35672321 PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [//pubmed.gov/34987166 PubMed] [//netbiolab.org/wiki/files/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [//pubmed.gov/34747468 PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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] [//netbiolab.org/wiki/files/glucose_germrate.txt Supplementary File 1] [//netbiolab.org/wiki/files/glucose_sig_accessions.txt Supplementary File 2]
 

==2020 (9)==
*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]
 
*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]
 
*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 [//netbiolab.org/wiki/files/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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2026-04-15T12:29:26Z

Il1001: /* 2026 (8) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (8)==
*134. Metformin beyond Glycemic Control: New Mechanistic Insights and Expanding Therapeutic Horizons, '''''Under Review'''''
 
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Under Review'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Revision'''''
 
*131. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*130. Yura Seo*, Yoon Dae Han, Linda Bojmar, Kyung-A Kim, Yurin Seo, Taeyul K. Kim, Suho Lee, Yeleem Kim, Hye Bin Choi, Yujin H. Lim, Chae Hyun Kim, Alexander Sandberg, Chuanwen Fan, Pernille Lauritzen, Henrik Molina, Christopher Peralta, Jacob B. Geri, Colin Burdette, Dai Hoon Han, Heon Yung Gee, '''Insuk Lee''', Jeon-Soo Shin, Hyunwook Kim, Leon Li, Gabriel C. Tobias, Inbal Wortzel, Sang Joon Shin, Hyo-Il Jung, Min Goo Lee, Soonmyung Paik, Robert E. Schwartz, Joong Bae Ahn, David Lyden, Han Sang Kim**, Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Journal of Extracellular Vesicles''''' 2026 Apr;15(4):e70278 [https://pubmed.ncbi.nlm.nih.gov/41979056/ pubmed]
 
*129. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Nature Communications''''' 2026 Apr 14;17(1):3467 [https://pubmed.ncbi.nlm.nih.gov/41836788/ pubmed]
 
*128. '''Jun Hyung Cha*, Sol-Ah Jeong*''', Byoung-Seok Ye, '''Insuk Lee**, Bock-Young Jung**''', Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia, '''''Journal of Oral Microbiology''''' 2026 Mar 11;18(1):2643036 [https://pubmed.ncbi.nlm.nih.gov/41836788/ pubmed]
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [//pubmed.gov/36289209 PubMed] [//www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [//pubmed.gov/36291657 PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [//pubmed.gov/36057640 PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [//pubmed.gov/35672321 PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [//pubmed.gov/34987166 PubMed] [//netbiolab.org/wiki/files/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [//pubmed.gov/34747468 PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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] [//netbiolab.org/wiki/files/glucose_germrate.txt Supplementary File 1] [//netbiolab.org/wiki/files/glucose_sig_accessions.txt Supplementary File 2]
 

==2020 (9)==
*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]
 
*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]
 
*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 [//netbiolab.org/wiki/files/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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2026-04-14T23:49:39Z

Il1001: /* 2026 (8) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (8)==
*134. Metformin beyond Glycemic Control: New Mechanistic Insights and Expanding Therapeutic Horizons, '''''Under Review'''''
 
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Under Review'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Revision'''''
 
*131. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*130. Yura Seo*, Yoon Dae Han, Linda Bojmar, Kyung-A Kim, Yurin Seo, Taeyul K. Kim, Suho Lee, Yeleem Kim, Hye Bin Choi, Yujin H. Lim, Chae Hyun Kim, Alexander Sandberg, Chuanwen Fan, Pernille Lauritzen, Henrik Molina, Christopher Peralta, Jacob B. Geri, Colin Burdette, Dai Hoon Han, Heon Yung Gee, '''Insuk Lee''', Jeon-Soo Shin, Hyunwook Kim, Leon Li, Gabriel C. Tobias, Inbal Wortzel, Sang Joon Shin, Hyo-Il Jung, Min Goo Lee, Soonmyung Paik, Robert E. Schwartz, Joong Bae Ahn, David Lyden, Han Sang Kim**, Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Journal of Extracellular Vesicles''''' 2026 Apr;15(4):e70278 [https://pubmed.ncbi.nlm.nih.gov/41979056/ pubmed]
 
*129. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Nature Communications''''' [https://pubmed.ncbi.nlm.nih.gov/41836788/ pubmed]
 
*128. '''Jun Hyung Cha*, Sol-Ah Jeong*''', Byoung-Seok Ye, '''Insuk Lee**, Bock-Young Jung**''', Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia, '''''Journal of Oral Microbiology''''' 2026 Mar 11;18(1):2643036 [https://pubmed.ncbi.nlm.nih.gov/41836788/ pubmed]
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [//pubmed.gov/36289209 PubMed] [//www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [//pubmed.gov/36291657 PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [//pubmed.gov/36057640 PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [//pubmed.gov/35672321 PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [//pubmed.gov/34987166 PubMed] [//netbiolab.org/wiki/files/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [//pubmed.gov/34747468 PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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] [//netbiolab.org/wiki/files/glucose_germrate.txt Supplementary File 1] [//netbiolab.org/wiki/files/glucose_sig_accessions.txt Supplementary File 2]
 

==2020 (9)==
*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]
 
*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]
 
*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 [//netbiolab.org/wiki/files/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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2026-04-14T10:33:26Z

Il1001: /* 2026 (8) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (8)==
*134. Metformin beyond Glycemic Control: New Mechanistic Insights and Expanding Therapeutic Horizons, '''''Under Review'''''
 
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Under Review'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Revision'''''
 
*131. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*130. Yura Seo*, Yoon Dae Han, Linda Bojmar, Kyung-A Kim, Yurin Seo, Taeyul K. Kim, Suho Lee, Yeleem Kim, Hye Bin Choi, Yujin H. Lim, Chae Hyun Kim, Alexander Sandberg, Chuanwen Fan, Pernille Lauritzen, Henrik Molina, Christopher Peralta, Jacob B. Geri, Colin Burdette, Dai Hoon Han, Heon Yung Gee, '''Insuk Lee''', Jeon-Soo Shin, Hyunwook Kim, Leon Li, Gabriel C. Tobias, Inbal Wortzel, Sang Joon Shin, Hyo-Il Jung, Min Goo Lee, Soonmyung Paik, Robert E. Schwartz, Joong Bae Ahn, David Lyden, Han Sang Kim**, Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Journal of Extracellular Vesicles''''' [https://pubmed.ncbi.nlm.nih.gov/41836788/ pubmed]
 
*129. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Nature Communications''''' [https://pubmed.ncbi.nlm.nih.gov/41836788/ pubmed]
 
*128. '''Jun Hyung Cha*, Sol-Ah Jeong*''', Byoung-Seok Ye, '''Insuk Lee**, Bock-Young Jung**''', Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia, '''''Journal of Oral Microbiology''''' 2026 Mar 11;18(1):2643036 [https://pubmed.ncbi.nlm.nih.gov/41836788/ pubmed]
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [//pubmed.gov/36289209 PubMed] [//www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [//pubmed.gov/36291657 PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [//pubmed.gov/36057640 PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [//pubmed.gov/35672321 PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [//pubmed.gov/34987166 PubMed] [//netbiolab.org/wiki/files/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [//pubmed.gov/34747468 PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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] [//netbiolab.org/wiki/files/glucose_germrate.txt Supplementary File 1] [//netbiolab.org/wiki/files/glucose_sig_accessions.txt Supplementary File 2]
 

==2020 (9)==
*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]
 
*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]
 
*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 [//netbiolab.org/wiki/files/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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

People

2026-04-13T10:11:19Z

Il1001: /* Scientists & Research Staff */

__NOTOC__
=='''Scientists & Research Staff'''==
{|border="0" width="1080"
|align="center"|[[File:prof_Insuk_fixed.png|100px|link=people:IS_Lee]]
|align="center"|[[File:SM_fixed.png|100px|link=people:SM_Yang]]
|align="center"|[[File:JunHyeong_fixed.png|100px|link=People:Jun_Hyung_Cha]]
|align="center"|[[File:Ilseok_fixed.png|100px|link=People:IS_Choi]]
|align="center"|[[File:JunYeong_fixed.png|100px|link=People:Junyeong_Ma]]
|align="center"|[[File:Hanjune_fixed.png|100px|link=People:Han-June_KIM]]
|align="center"|[[File:EuiJeong_fixed.png|100px|link=People:EuiJeong_Sung]]
|align="center"|[[File:Sehun_fixed.png|100px|link=People:Sehun_Ahn]]
|-

|width=160px; align="center"|[[people:IS_Lee|<big>'''Insuk Lee'''</big>]]
|width=160px; align="center"|[[people:SM_Yang|<big>'''Sunmo Yang'''</big>]]
|width=160px; align="center"|[[People:Jun_Hyung_Cha|<big>'''Jun Hyung Cha'''</big>]]
|width=160px; align="center"|[[People:IS_Choi|<big>'''Ilseok Choi'''</big>]]
|width=160px; align="center"|[[People:Junyeong_Ma|<big>'''Junyeong Ma'''</big>]]
|width=160px; align="center"|[[People:Hanjune_Kim|<big>'''Hanjune Kim'''</big>]]
|width=160px; align="center"|[[People:Euijeong_Sung|<big>'''Euijeong Sung'''</big>]]
|width=160px; align="center"|[[People:Sehun_Ahn|<big>'''Sehun Ahn'''</big>]]
|-

|align="center"|[[people:IS_Lee|Principal Investigator Professor]]
|align="center"|[[people:SM_Yang|Bioinformatics Programmer & Sys. Admin]]
|align="center"|[[People:Jun_Hyung_Cha|Postdoc Fellow (Microbiome) ]]
|align="center"|[[People:IS_Choi|Ph.D candidate (Single-cell Biology) (2020.9 - )]]

|align="center"|[[People:Junyeong_Ma|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Hanjune_Kim|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Euijeong_Sung|Ph.D candidate (Single-cell Biology) (2021.9 - )]]
|align="center"|[[People:Sehun_Ahn|Ph.D candidate (Microbiome) (2022.3 - )]]

|}
{|border="0" width="1080"
|align="center"|[[File:Jungyeon_fixed.png|100px|link=People:Jungyeon_Kim]]
|align="center"|[[File:Yerin_fixed.png|100px|link=People:Yerin_Kim]]
|align="center"|[[File:Yurim_fixed_(2).jpg|100px|link=People:Yurim_Jung]]
|align="center"|[[File:HaeBeen_fixed.jpg|100px|link=People:Hae_Been_lee]]
|align="center"|[[File:Sebin_fixed.jpg|100px|link=People:Sebin_Lim]]
|align="center"|[[File:Yunyeong_fixed.png|100px|link=People:Yunyeong_Jang]]
|align="center"|[[File:Jonghyun_fixed.png|100px|link=People:Jonghyun_Hwang]]
|-
|width=160px; align="center"|[[People:Jungyeon_Kim|<big>'''Jungyeon Kim'''</big>]]
|width=160px; align="center"|[[People:Yerin_Kim|<big>'''Yerin Kim'''</big>]]
|width=160px; align="center"|[[People:Yurim_Jung|<big>'''Yurim Jung'''</big>]]
|width=160px; align="center"|[[People:Hae_Been_lee|<big>'''Hae Been Lee'''</big>]]
|width=160px; align="center"|[[People:Sebin_Lim|<big>'''Sebin Lim'''</big>]]
|width=160px; align="center"|[[People:Yunyeong_Jang|<big>'''Yunyeong Jang'''</big>]]
|width=160px; align="center"|[[People:Jonghyun_Hwang|<big>'''Jonghyun Hwang'''</big>]]

|-
|align="center"|[[People:Jungyeon_Kim|Ph.D candidate (Microbiome) (2023.3 - )]]
|align="center"|[[People:Yerin_Kim|Integrated Ph.D course (Microbiome) (2024.3 - )]]
|align="center"|[[People:Yurim_Jung|Integrated Ph.D course (Single-cell Biology) (2024.9 - )]]
|align="center"|[[People:Hae_Been_lee|Integrated Ph.D course (Microbiome) (2024.9 - )]]
|align="center"|[[People:Sebin_Lim|Integrated Ph.D course (Microbiome) (2025.3 - )]]
|align="center"|[[People:Yunyeong_Jang|Master course (Drug Discovery) (2026.3 - )]]
|align="center"|[[People:Jonghyun_Hwang|Master course (Microbiome) (2026.3 - )]]
|}

=='''Administrative Assistant'''==

=='''Undergraduate Students'''==
*Zunu An
*Seung Wan Jeon
*Sung Min Kim
*Zixuan Guo
*Hyeonjin Kim
*Eunjeong Kim

=='''Alumni'''==
*'''Former Post-docs and Staff Scientists'''
**1. Taeyun Oh (2009.5-2011.12), currently Senior Researcher at Cowellbiogim, Korea
**2. Sohyun Hwang (2010.3-2015.8), currently Professor at [https://grad.cha.ac.kr/%ed%99%a9%ec%86%8c%ed%98%84/ Department of Biomedical Science, CHA University], Korea [https://scholar.google.com/citations?user=z5yC9cwAAAAJ&hl=en Google Scholar] (차의과대학 의과학과 교수)
**3. Samuel Beck (2011.2-2011.12), currently Associate Professor at Boston University, USA, [https://beck310.wixsite.com/becklab Lab Homepage] (미 보스턴 대학교 부교수)
**4. Jawon Song (2011.1-2012.5), currently Research Associate at [https://www.tacc.utexas.edu/about/directory/jawon-song Texas Advanced Computing Center], Austin, TX, USA [https://scholar.google.com/citations?user=wv61wGoAAAAJ&hl=en Google Scholar] (미국 텍사스슈퍼컴퓨팅센터 선임연구원)
**5. Yoonhee Ko (2012.8-2014.2), currently Associate Professor at [https://hufsbiomed.weebly.com/ Department of Biomedical Engineering, Hankuk University of Foreign Studies], Korea [https://scholar.google.com/citations?user=GBxCYX8AAAAJ&hl=en Google Scholar] (한국외국어대 바이오공학과 교수)
**6. Jonghoon Lee (2013.10-2014.2), currently Professor at [https://www.gachon.ac.kr/foodbiotech/6142/subview.do Department of Food Biotechnology, Gachon University], Korea (가천대학교 식품생명공학과 교수)
**7. Jung Eun Shim (2009.8-2017.11), currently Staff Scientist at Yonsei Genomics Center Bioinformatics Data Analysis Core (연세의료원 유전체센터 생명정보분석코어 책임연구원)

*'''Former Graduate Students (Ph.D)'''
**1. Junha Shin (2008.9-2014.2), PhD; currently Scientist at [https://wid.wisc.edu/people/junha-shin/ Wisconsin Institute for Discovery], USA (미국 위스콘신 대학연구소 연구원)
**2. Hanhae Kim (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**3. Ara Cho (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**4. Eiru Kim (2010.9-2016.8), PhD; currently Senior Expert in Data Science, [https://www.gnf.org/ The Genomics Institute of the Novartis Research Foundation], San Diego, USA (노바티스 선임데이터분석연구원)
**5. Tak Lee (2011.3-2017.2), PhD; currently Senior Bioinformatician, [https://www.mpipz.mpg.de/en Max Planck Institute for Plant Breeding Research] (독일 막스플랭크 연구소 선임생명정보학자)
**6. Heonjong Han (2013.3~2019.8), PhD; currently Bioinformatics engineer at [https://3billion.io/ 3billion] (바이오기업 데이터사이언티스트)
**7. Kyungsoo Kim (2013.3~2020.2), PhD; currently Research Professor at Severance Hospital (강남세브란스의료원 유방암센터 연구교수)
**8. Jae-Won Cho (2016.9~2021.2), PhD; currently Assistant Professor at [https://ibb.hanyang.ac.kr/ Hanyang Institute of Bioscience and Biotechnology] (한양대학교 한양생명과학기술원 조교수)
**9. Chan Yeong Kim (2015.3~2021.2), PhD; currently Postdoc Fellow at European Molecular Biology Laboratory in Heidelberg [http://www.bork.embl.de/j/ Bork Group] (유럽연합분자생물학연구소 박사후 연구원)
**10. Sungho Lee (2017.3-2024.2), PhD; currently Data Scientist at [http://www.mogam.re.kr/kor/ MOGAM Institute for Biomedical Research] (목암생명과학연구소, (주)녹십자 출연 연구소, 선임연구원)
**11. Junha Cha (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://dna-discovery.stanford.edu/ Prof. Hanlee P. Ji Lab](미국 스탠퍼드대학교 박사후연구원)
**12. Seungbyn Baek (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://kundajelab.github.io/ Prof. Anshul Kundaje Lab](미국 스탠퍼드대학교 박사후연구원)
**13. Nayeon Kim (2019.9-2025.2), PhD; currently Postdoc Fellow at KAIST InnoCORE Research Group (과학기술원 InnoCORE 초거대언어모델 혁신 연구단, 박사후연구원)
**14. Jun Hyung Cha (2020.9-2026.2), PhD;

*'''Former Graduate Students (Master's degree)'''
**1. Sun-Gou Ji (2009.9-2011.8), M.Eng.; PhD from University of Cambridge (Sanger Genome center); currently Vice President, Computational Genetics at [https://bridgebio.com/ BridgeBio Pharma], Boston, USA (미 바이오기업 부대표)
**2. Hyojin Kim (2013.3-2015.2), M.Eng.; PhD from University of Aachen; currently Scientist at Bayer, Germany [https://www.linkedin.com/in/hyojin-kim-b3bb711ab Linkedin] (독일 바이엘 제약회사 선임 연구원)
**3. Hongseok Shim (2013.9-2015.8), M.Eng.; currently PhD student, Arizona State University, Biomedical Informatics program (애리조나주립대 생물정보학 박사과정)
**4. Sunmo Yang (2014.9-2017.2), M.Eng. currently Bioinformatics programmer, Yonsei University (연세대 네트워크생명공학 연구실 책임데이터연구원)
**5. Muyoung Lee (2016.3-2018.2), M.Eng. currently PhD student, University of Texas at Austin, Cellular and Molecular Biology Program (텍사스주립대 생물정보학 박사과정)
**6. Jiwon Yu (2021.9-2023.8), M.Eng. currently Data Scientist at [https://www.samsungbioepis.com/kr/index.do SAMSUNG BIOEPIS] (삼성바이오에피스 데이터사이언티스트)
**7. Geon_Koh (2022.9-2025.2), M.Eng. currently Researcher at Gachon University, College of Medicine (가천의대 시스템생물학 연구실 연구원)
**8. Wonjong Kim (2023.3-2025.8), M.Eng. currently Researcher at [https://samsungbiologics.com/ SAMSUNG Biologics] (삼성바이오로직스 연구원)

*'''Former Visiting Scientists/Students'''
**1. Minkyung Shin (2012.3-2012.7), went to University of Southern California graduate school
**2. Paul Chung (2012 summer), currently work at [https://about.meta.com/ Meta], USA
**3. Hyunjin Cho (2014 summer), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA
**4. Michael Chung (2016.8-2016.12), currently work at [https://about.meta.com/ Meta], USA

*'''Former Undergraduate Students'''
**1. Ila Shin, went to medical school (Yonsei Univ.) Currently Professor, Kyunghee University School of Medicine (경희대학교 의과대학 교수)
**2. Yoonkyung Ko
**3. Sangyo Park, went to law school (Kyounghee Univ.)
**4. Jayoon Shin, went to medical school (Pusan National Univ.)
**5. Dongjoo Sun, went to dental school (Wongwang Univ.)
**6. Eulsoo Kim
**7. Myungwhan Lee, went to medical school (Yonsei Univ.)
**8. Moonhee Lee, went to graduate school (University of Amsterdam, Netherlands)
**9. Jinhyun Ju, went to graduate school (Cornell Medical School, Computational Systems Biology); Currently Principal Computational Biologist, Cancer Genomics at [https://bridgebio.com/ BridgeBio Pharma], Seattle, USA (미 바이오기업 선임연구원)
**10. Haeyoung Shin, went to graduate school (Brown University, Computational Neuroscience); Currently Professor, Seoul National University (서울대학교 생명과학부 교수)
**11. Joonghee Soh, went to graduate school (KAIST, Culture Technology)
**12. Hee Jung Cho, went to graduate school (UC Berkeley)
**13. TaeHwan Kim, went to medical school
**14. Joohyung Kim, went to medical school (Kyungpook National Univ.)
**15. Donghyun Shin, went to medical school (Yonsei Univ.)
**16. Byunghee Kang (2015 spring - 2016 summer), went to graduate school (PosTech)
**17. Sunphil Kim (2016 winter)
**18. Jaeho Shim (2016 winter)
**19. Seunghyun Shin (2016 spring)
**20. Aejoo Hong (2016 spring)
**21. Changbae Bang (2016 summer), went to medical school (Yonsei Univ.)
**22. Seoyoung Choi (2016 summer)
**23. Dabin Jung (2016 summer)
**24. Boreum Nam (2016 summer)
**25. Seungun Lee (2016 summer)
**26. Yeaji Kim (2016 summer and fall)
**27. Sangyoung Lee (2017 winter)
**28. Heejun Jang (2017 winter & spring), went to KIST as Research Assistant
**29. Jungha Lee (2017 summer), went to graduate school (Seoul National Univ.)
**30. Seunghyun Wang (2017 summer), went to graduate school (KAIST)
**31. Dong-Min Yang (2017 fall)
**32. Doo-Hee Lee (2017 fall)
**33. Suk-Jae Han (2018 winter)
**34. Ji-Eun Han (2018 winter)
**35. Yuri Ko (2018 spring)
**36. Sung-Woo Kim (2018 spring)
**37. Woosung Kwon (2018 summer)
**38. Soyun Kong (2018 summer)
**39. Hojeong Keum (2018 summer and fall)
**40. Sungjun Lim (2018 summer and fall)
**41. Jiyoon Lee (2018 summer and fall)
**42. Ilseok Choi(2019 winter, spring, summer and fall, 2020 winter, spring)
**43. Junik Park (2019 winter)
**44. Lee Yoo (2019 winter & spring)
**45. Yeonwha Kim (2019 winter & spring)
**46. Sohee Kim (2019 spring)
**47. Juseong Lee (2019 spring)
**48. Junyoung Yang (2019 spring & summer)
**49. Junyeong Ma (2019 summer, 2020 winter, summer, fall, 2021 winter)
**50. Dayeon Jung (2019 summer)
**51. Hanjoon Kim (2019 summer, 2021 winter)
**52. Hyungjin Kim (2020 winter, spring)
**53. Sujin Hyun (2020 winter)
**54. Hyuki Lee (2020 winter)
**55. Donghwan Lee (2020 winter)
**56. Jun Hyung Cha (2020 spring, summer)
**57. Jiwon Yu (2020 summer, 2021 Spring, summer)
**58. Dong Seok Kim (2020 summer)
**59. Donggeun Lee (2020 summer)
**60. Sehun Ahn (2020 summer, 2021 winter, spring, summer, 2022 winter)
**61. Jiho Kim (2020 summer)
**62. Euijung Seong (2020 fall, 2021 spring, summer)
**63. Junhan Kim (2021 winter & spring)
**64. Suyong Choi (2021 winter)
**65. Sujin Pyeon (2021 Spring)
**66. Hyeon Hee Ji (2021 Spring)
**67. Semin Kim (2021 Summer)
**68. Su Hwan Kim (2021 Summer)
**69. Yongbin Kim (2021 Summer)
**70. Nan Park (2021 Summer)
**71. Hoyong Jung (2021 Summer)
**72. Ingyeong Koh (2021 Summer)
**73. Jongbin Jeong (2022 Winter)
**74. Sungchul Yang (2022 Winter, Spring, Summer)
**75. Hyojung Lee (2022 Winter, Spring)
**76. Jun Hyeong Kim (2022 Winter, Spring)
**77. Young Ji Roh (2022 Spring, Summer)
**78. Geon Koh (2022 Spring, Summer)
**79. Hayoung Kang (2022 Summer, 2023 Spring)
**80. Won Jong Kim (2022 Summer, Fall, 2023 Winter)
**81. Christian Lee (2022 Summer)
**82. Je Yun Kang (2022 Summer)
**83. Sumin Lee (2022 Fall)
**84. Jungyeon Kim (2022 Fall, 2023 Winter)
**85. Seol Song (2023 Winter)
**86. Soyeon Kim (2023 Summer)
**87. Sieun Park (2023 Summer)
**88. Gunhyeong Lee (2023 Summer)
**89. Yunseo Han (2023 Summer)
**90. Jae Hyun Kim (2023 Summer)
**91. Jeong-min Seo (2023 Summer)
**92. Yerin Kim (2023 Fall, 2024 Winter)
**93. Sang Min Park (2024 Winter)
**94. Minsun Seo (2024 Winter)
**95. Jaeryun Sim (2024 Winter)
**96. Sun Min Lim (2024 Winter)
**97. Yurim Jung (2024 Spring, Summer)
**98. Hae Been Lee (2024 Spring, Summer)
**99. Zunu An (2024 Summer, Fall, 2025 Winter, Spring, Summer, Fall, 2026 Winter)
**100. Se Bin Lim (2024 Summer, Fall, 2025 Winter)
**101. Sang Min Yoon (2024 Summer)
**102. Yena Kim (2024 Summer)
**103. Kang Eon Lee (2024 Fall)
**104. Soyoon Park (2025 Winter)
**105. Sojung Lee (2025 Winter)
**106. Leanne Ma (2025 Winter)
**107. Seung Wan Jeon (2025 Summer, Fall, 2026 Winter)
**108. Joongun Lee (2025 Summer)
**109. Minseo Kim (2025 Summer)
**110. Hong Kyu Park (2025 Summer)
**111. Yunyeong Jang (2025 Fall, 2026 Winter)
**112. Jong Hyun Hwang (2025 Fall, 2026 Winter)
**113. Gyuweon Park (2025 Fall)
**114. Sung Min Kim (2026 Winter)
**115. Zixuan Guo (2026 Winter)
**116. Hyeonjin Kim (2026 Winter)
**117. Eunjeong Kim (2026 Winter)

Publications

2026-03-26T00:37:18Z

Il1001: /* 2026 (8) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (8)==
*134. Metformin beyond Glycemic Control: New Mechanistic Insights and Expanding Therapeutic Horizons, '''''Under Review'''''
 
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Under Review'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Revision'''''
 
*131. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*130. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Journal of Extracellular Vesicles''''' Accepted
 
*129. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Nature Communications''''' Accepted
 
*128. '''Jun Hyung Cha*, Sol-Ah Jeong*''', Byoung-Seok Ye, '''Insuk Lee**, Bock-Young Jung**''', Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia, '''''Journal of Oral Microbiology''''' 2026 Mar 11;18(1):2643036 [https://pubmed.ncbi.nlm.nih.gov/41836788/ pubmed]
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [//pubmed.gov/36289209 PubMed] [//www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [//pubmed.gov/36291657 PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [//pubmed.gov/36057640 PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [//pubmed.gov/35672321 PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [//pubmed.gov/34987166 PubMed] [//netbiolab.org/wiki/files/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [//pubmed.gov/34747468 PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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] [//netbiolab.org/wiki/files/glucose_germrate.txt Supplementary File 1] [//netbiolab.org/wiki/files/glucose_sig_accessions.txt Supplementary File 2]
 

==2020 (9)==
*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]
 
*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]
 
*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 [//netbiolab.org/wiki/files/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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2026-03-25T01:29:37Z

Il1001: /* 2026 (8) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (8)==
*134. Metformin beyond Glycemic Control: New Mechanistic Insights and Expanding Therapeutic Horizons, '''''Under Review'''''
 
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Under Review'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Revision'''''
 
*131. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*130. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Accepted'''''
 
*129. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Nature Communications''''' Accepted
 
*128. '''Jun Hyung Cha*, Sol-Ah Jeong*''', Byoung-Seok Ye, '''Insuk Lee**, Bock-Young Jung**''', Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia, '''''Journal of Oral Microbiology''''' 2026 Mar 11;18(1):2643036 [https://pubmed.ncbi.nlm.nih.gov/41836788/ pubmed]
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [//pubmed.gov/36289209 PubMed] [//www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [//pubmed.gov/36291657 PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [//pubmed.gov/36057640 PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [//pubmed.gov/35672321 PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [//pubmed.gov/34987166 PubMed] [//netbiolab.org/wiki/files/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [//pubmed.gov/34747468 PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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] [//netbiolab.org/wiki/files/glucose_germrate.txt Supplementary File 1] [//netbiolab.org/wiki/files/glucose_sig_accessions.txt Supplementary File 2]
 

==2020 (9)==
*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]
 
*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]
 
*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 [//netbiolab.org/wiki/files/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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

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2026-03-25T01:28:26Z

Il1001:

The Network Biology Laboratory is currently seeking talented '''graduate students'''.

We welcome applicants from diverse educational and research backgrounds.

The ideal candidate must be a highly motivated individual who can enjoy working in multidisciplinary research environments.

We are currently interested in applicants for the following research areas.
*AI Bio Research
*Computational Metagenomics
*Foundation Models in Biology
*AI-based drug discovery

'''How to apply''':
Email your current CV to Insuk Lee

Positions Available

2026-03-25T01:26:10Z

Il1001:

The Network Biology Laboratory is currently seeking talented '''graduate students'''.

We welcome applicants from diverse educational and research backgrounds.

The ideal candidate must be a highly motivated individual who can enjoy working in multidisciplinary research environments.

We are currently interested in applicants for the following research areas.
*Cancer Genomics and Systems Biology
*Cancer Immunology
*Single-cell genomics
*Human Gut Microbiome Study

'''How to apply''':
Email your current CV to Insuk Lee

Publications

2026-03-21T02:07:04Z

Il1001: /* 2026 (8) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (8)==
*134. Metformin beyond Glycemic Control: New Mechanistic Insights and Expanding Therapeutic Horizons, '''''Under Review'''''
 
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Under Review'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Revision'''''
 
*131. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*130. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*129. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Nature Communications''''' Accepted
 
*128. '''Jun Hyung Cha*, Sol-Ah Jeong*''', Byoung-Seok Ye, '''Insuk Lee**, Bock-Young Jung**''', Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia, '''''Journal of Oral Microbiology''''' 2026 Mar 11;18(1):2643036 [https://pubmed.ncbi.nlm.nih.gov/41836788/ pubmed]
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [//pubmed.gov/36289209 PubMed] [//www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [//pubmed.gov/36291657 PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [//pubmed.gov/36057640 PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [//pubmed.gov/35672321 PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [//pubmed.gov/34987166 PubMed] [//netbiolab.org/wiki/files/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [//pubmed.gov/34747468 PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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] [//netbiolab.org/wiki/files/glucose_germrate.txt Supplementary File 1] [//netbiolab.org/wiki/files/glucose_sig_accessions.txt Supplementary File 2]
 

==2020 (9)==
*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]
 
*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]
 
*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 [//netbiolab.org/wiki/files/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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

People

2026-03-18T06:41:43Z

Il1001: /* Alumni */

__NOTOC__
=='''Scientists & Research Staff'''==
{|border="0" width="1080"
|align="center"|[[File:prof_Insuk_fixed.png|100px|link=people:IS_Lee]]
|align="center"|[[File:SM_fixed.png|100px|link=people:SM_Yang]]
|align="center"|[[File:Ilseok_fixed.png|100px|link=People:IS_Choi]]
|align="center"|[[File:JunHyeong_fixed.png|100px|link=People:Jun_Hyung_Cha]]
|align="center"|[[File:JunYeong_fixed.png|100px|link=People:Junyeong_Ma]]
|align="center"|[[File:Hanjune_fixed.png|100px|link=People:Han-June_KIM]]
|align="center"|[[File:EuiJeong_fixed.png|100px|link=People:EuiJeong_Sung]]
|-

|width=160px; align="center"|[[people:IS_Lee|<big>'''Insuk Lee'''</big>]]
|width=160px; align="center"|[[people:SM_Yang|<big>'''Sunmo Yang'''</big>]]
|width=160px; align="center"|[[People:IS_Choi|<big>'''Ilseok Choi'''</big>]]
|width=160px; align="center"|[[People:Jun_Hyung_Cha|<big>'''Jun Hyung Cha'''</big>]]
|width=160px; align="center"|[[People:Junyeong_Ma|<big>'''Junyeong Ma'''</big>]]
|width=160px; align="center"|[[People:Hanjune_Kim|<big>'''Hanjune Kim'''</big>]]
|width=160px; align="center"|[[People:Euijeong_Sung|<big>'''Euijeong Sung'''</big>]]
|-

|align="center"|[[people:IS_Lee|Principal Investigator Professor]]
|align="center"|[[people:SM_Yang|Bioinformatics Programmer & Sys. Admin]]
|align="center"|[[People:IS_Choi|Ph.D candidate (Single-cell Biology) (2020.9 - )]]
|align="center"|[[People:Jun_Hyung_Cha|Ph.D candidate (Microbiome) (2020.9 - )]]
|align="center"|[[People:Junyeong_Ma|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Hanjune_Kim|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Euijeong_Sung|Ph.D candidate (Single-cell Biology) (2021.9 - )]]
|}
{|border="0" width="1080"

|align="center"|[[File:Sehun_fixed.png|100px|link=People:Sehun_Ahn]]
|align="center"|[[File:Jungyeon_fixed.png|100px|link=People:Jungyeon_Kim]]
|align="center"|[[File:Yerin_fixed.png|100px|link=People:Yerin_Kim]]
|align="center"|[[File:Yurim_fixed_(2).jpg|100px|link=People:Yurim_Jung]]
|align="center"|[[File:HaeBeen_fixed.jpg|100px|link=People:Hae_Been_lee]]
|align="center"|[[File:Sebin_fixed.jpg|100px|link=People:Sebin_Lim]]
|-
|width=160px; align="center"|[[People:Sehun_Ahn|<big>'''Sehun Ahn'''</big>]]
|width=160px; align="center"|[[People:Jungyeon_Kim|<big>'''Jungyeon Kim'''</big>]]
|width=160px; align="center"|[[People:Yerin_Kim|<big>'''Yerin Kim'''</big>]]
|width=160px; align="center"|[[People:Yurim_Jung|<big>'''Yurim Jung'''</big>]]
|width=160px; align="center"|[[People:Hae_Been_lee|<big>'''Hae Been Lee'''</big>]]
|width=160px; align="center"|[[People:Sebin_Lim|<big>'''Sebin Lim'''</big>]]
|-
|align="center"|[[People:Sehun_Ahn|Ph.D candidate (Microbiome) (2022.3 - )]]
|align="center"|[[People:Jungyeon_Kim|Integrated Ph.D candidate (Microbiome) (2023.3 - )]]
|align="center"|[[People:Yerin_Kim|Integrated Ph.D course (Microbiome) (2024.3 - )]]
|align="center"|[[People:Yurim_Jung|Integrated Ph.D course (Single-cell Biology) (2024.9 - )]]
|align="center"|[[People:Hae_Been_lee|Integrated Ph.D course (Microbiome) (2024.9 - )]]
|align="center"|[[People:Sebin_Lim|Integrated Ph.D course (Microbiome) (2025.3 - )]]
|}

=='''Administrative Assistant'''==

=='''Undergraduate Students'''==
*Zunu An
*Seung Wan Jeon
*Yunyeong Jang
*Jong Hyun Hwang
*Sung Min Kim
*Zixuan Guo
*Hyeonjin Kim
*Eunjeong Kim

=='''Alumni'''==
*'''Former Post-docs and Staff Scientists'''
**1. Taeyun Oh (2009.5-2011.12), currently Senior Researcher at Cowellbiogim, Korea
**2. Sohyun Hwang (2010.3-2015.8), currently Professor at [https://grad.cha.ac.kr/%ed%99%a9%ec%86%8c%ed%98%84/ Department of Biomedical Science, CHA University], Korea [https://scholar.google.com/citations?user=z5yC9cwAAAAJ&hl=en Google Scholar] (차의과대학 의과학과 교수)
**3. Samuel Beck (2011.2-2011.12), currently Associate Professor at Boston University, USA, [https://beck310.wixsite.com/becklab Lab Homepage] (미 보스턴 대학교 부교수)
**4. Jawon Song (2011.1-2012.5), currently Research Associate at [https://www.tacc.utexas.edu/about/directory/jawon-song Texas Advanced Computing Center], Austin, TX, USA [https://scholar.google.com/citations?user=wv61wGoAAAAJ&hl=en Google Scholar] (미국 텍사스슈퍼컴퓨팅센터 선임연구원)
**5. Yoonhee Ko (2012.8-2014.2), currently Associate Professor at [https://hufsbiomed.weebly.com/ Department of Biomedical Engineering, Hankuk University of Foreign Studies], Korea [https://scholar.google.com/citations?user=GBxCYX8AAAAJ&hl=en Google Scholar] (한국외국어대 바이오공학과 교수)
**6. Jonghoon Lee (2013.10-2014.2), currently Professor at [https://www.gachon.ac.kr/foodbiotech/6142/subview.do Department of Food Biotechnology, Gachon University], Korea (가천대학교 식품생명공학과 교수)
**7. Jung Eun Shim (2009.8-2017.11), currently Staff Scientist at Yonsei Genomics Center Bioinformatics Data Analysis Core (연세의료원 유전체센터 생명정보분석코어 책임연구원)

*'''Former Graduate Students (Ph.D)'''
**1. Junha Shin (2008.9-2014.2), PhD; currently Scientist at [https://wid.wisc.edu/people/junha-shin/ Wisconsin Institute for Discovery], USA (미국 위스콘신 대학연구소 연구원)
**2. Hanhae Kim (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**3. Ara Cho (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**4. Eiru Kim (2010.9-2016.8), PhD; currently Senior Expert in Data Science, [https://www.gnf.org/ The Genomics Institute of the Novartis Research Foundation], San Diego, USA (노바티스 선임데이터분석연구원)
**5. Tak Lee (2011.3-2017.2), PhD; currently Senior Bioinformatician, [https://www.mpipz.mpg.de/en Max Planck Institute for Plant Breeding Research] (독일 막스플랭크 연구소 선임생명정보학자)
**6. Heonjong Han (2013.3~2019.8), PhD; currently Bioinformatics engineer at [https://3billion.io/ 3billion] (바이오기업 데이터사이언티스트)
**7. Kyungsoo Kim (2013.3~2020.2), PhD; currently Research Professor at Severance Hospital (강남세브란스의료원 유방암센터 연구교수)
**8. Jae-Won Cho (2016.9~2021.2), PhD; currently Assistant Professor at [https://ibb.hanyang.ac.kr/ Hanyang Institute of Bioscience and Biotechnology] (한양대학교 한양생명과학기술원 조교수)
**9. Chan Yeong Kim (2015.3~2021.2), PhD; currently Postdoc Fellow at European Molecular Biology Laboratory in Heidelberg [http://www.bork.embl.de/j/ Bork Group] (유럽연합분자생물학연구소 박사후 연구원)
**10. Sungho Lee (2017.3-2024.2), PhD; currently Data Scientist at [http://www.mogam.re.kr/kor/ MOGAM Institute for Biomedical Research] (목암생명과학연구소, (주)녹십자 출연 연구소, 선임연구원)
**11. Junha Cha (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://dna-discovery.stanford.edu/ Prof. Hanlee P. Ji Lab](미국 스탠퍼드대학교 박사후연구원)
**12. Seungbyn Baek (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://kundajelab.github.io/ Prof. Anshul Kundaje Lab](미국 스탠퍼드대학교 박사후연구원)
**13. Nayeon Kim (2019.9-2025.2), PhD; currently Postdoc Fellow at KAIST InnoCORE Research Group (과학기술원 InnoCORE 초거대언어모델 혁신 연구단, 박사후연구원)
**14. Jun Hyung Cha (2020.9-2026.2), PhD;

*'''Former Graduate Students (Master's degree)'''
**1. Sun-Gou Ji (2009.9-2011.8), M.Eng.; PhD from University of Cambridge (Sanger Genome center); currently Vice President, Computational Genetics at [https://bridgebio.com/ BridgeBio Pharma], Boston, USA (미 바이오기업 부대표)
**2. Hyojin Kim (2013.3-2015.2), M.Eng.; PhD from University of Aachen; currently Scientist at Bayer, Germany [https://www.linkedin.com/in/hyojin-kim-b3bb711ab Linkedin] (독일 바이엘 제약회사 선임 연구원)
**3. Hongseok Shim (2013.9-2015.8), M.Eng.; currently PhD student, Arizona State University, Biomedical Informatics program (애리조나주립대 생물정보학 박사과정)
**4. Sunmo Yang (2014.9-2017.2), M.Eng. currently Bioinformatics programmer, Yonsei University (연세대 네트워크생명공학 연구실 책임데이터연구원)
**5. Muyoung Lee (2016.3-2018.2), M.Eng. currently PhD student, University of Texas at Austin, Cellular and Molecular Biology Program (텍사스주립대 생물정보학 박사과정)
**6. Jiwon Yu (2021.9-2023.8), M.Eng. currently Data Scientist at [https://www.samsungbioepis.com/kr/index.do SAMSUNG BIOEPIS] (삼성바이오에피스 데이터사이언티스트)
**7. Geon_Koh (2022.9-2025.2), M.Eng. currently Researcher at Gachon University, College of Medicine (가천의대 시스템생물학 연구실 연구원)
**8. Wonjong Kim (2023.3-2025.8), M.Eng. currently Researcher at [https://samsungbiologics.com/ SAMSUNG Biologics] (삼성바이오로직스 연구원)

*'''Former Visiting Scientists/Students'''
**1. Minkyung Shin (2012.3-2012.7), went to University of Southern California graduate school
**2. Paul Chung (2012 summer), currently work at [https://about.meta.com/ Meta], USA
**3. Hyunjin Cho (2014 summer), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA
**4. Michael Chung (2016.8-2016.12), currently work at [https://about.meta.com/ Meta], USA

*'''Former Undergraduate Students'''
**1. Ila Shin, went to medical school (Yonsei Univ.) Currently Professor, Kyunghee University School of Medicine (경희대학교 의과대학 교수)
**2. Yoonkyung Ko
**3. Sangyo Park, went to law school (Kyounghee Univ.)
**4. Jayoon Shin, went to medical school (Pusan National Univ.)
**5. Dongjoo Sun, went to dental school (Wongwang Univ.)
**6. Eulsoo Kim
**7. Myungwhan Lee, went to medical school (Yonsei Univ.)
**8. Moonhee Lee, went to graduate school (University of Amsterdam, Netherlands)
**9. Jinhyun Ju, went to graduate school (Cornell Medical School, Computational Systems Biology); Currently Principal Computational Biologist, Cancer Genomics at [https://bridgebio.com/ BridgeBio Pharma], Seattle, USA (미 바이오기업 선임연구원)
**10. Haeyoung Shin, went to graduate school (Brown University, Computational Neuroscience); Currently Professor, Seoul National University (서울대학교 생명과학부 교수)
**11. Joonghee Soh, went to graduate school (KAIST, Culture Technology)
**12. Hee Jung Cho, went to graduate school (UC Berkeley)
**13. TaeHwan Kim, went to medical school
**14. Joohyung Kim, went to medical school (Kyungpook National Univ.)
**15. Donghyun Shin, went to medical school (Yonsei Univ.)
**16. Byunghee Kang (2015 spring - 2016 summer), went to graduate school (PosTech)
**17. Sunphil Kim (2016 winter)
**18. Jaeho Shim (2016 winter)
**19. Seunghyun Shin (2016 spring)
**20. Aejoo Hong (2016 spring)
**21. Changbae Bang (2016 summer), went to medical school (Yonsei Univ.)
**22. Seoyoung Choi (2016 summer)
**23. Dabin Jung (2016 summer)
**24. Boreum Nam (2016 summer)
**25. Seungun Lee (2016 summer)
**26. Yeaji Kim (2016 summer and fall)
**27. Sangyoung Lee (2017 winter)
**28. Heejun Jang (2017 winter & spring), went to KIST as Research Assistant
**29. Jungha Lee (2017 summer), went to graduate school (Seoul National Univ.)
**30. Seunghyun Wang (2017 summer), went to graduate school (KAIST)
**31. Dong-Min Yang (2017 fall)
**32. Doo-Hee Lee (2017 fall)
**33. Suk-Jae Han (2018 winter)
**34. Ji-Eun Han (2018 winter)
**35. Yuri Ko (2018 spring)
**36. Sung-Woo Kim (2018 spring)
**37. Woosung Kwon (2018 summer)
**38. Soyun Kong (2018 summer)
**39. Hojeong Keum (2018 summer and fall)
**40. Sungjun Lim (2018 summer and fall)
**41. Jiyoon Lee (2018 summer and fall)
**42. Ilseok Choi(2019 winter, spring, summer and fall, 2020 winter, spring)
**43. Junik Park (2019 winter)
**44. Lee Yoo (2019 winter & spring)
**45. Yeonwha Kim (2019 winter & spring)
**46. Sohee Kim (2019 spring)
**47. Juseong Lee (2019 spring)
**48. Junyoung Yang (2019 spring & summer)
**49. Junyeong Ma (2019 summer, 2020 winter, summer, fall, 2021 winter)
**50. Dayeon Jung (2019 summer)
**51. Hanjoon Kim (2019 summer, 2021 winter)
**52. Hyungjin Kim (2020 winter, spring)
**53. Sujin Hyun (2020 winter)
**54. Hyuki Lee (2020 winter)
**55. Donghwan Lee (2020 winter)
**56. Jun Hyung Cha (2020 spring, summer)
**57. Jiwon Yu (2020 summer, 2021 Spring, summer)
**58. Dong Seok Kim (2020 summer)
**59. Donggeun Lee (2020 summer)
**60. Sehun Ahn (2020 summer, 2021 winter, spring, summer, 2022 winter)
**61. Jiho Kim (2020 summer)
**62. Euijung Seong (2020 fall, 2021 spring, summer)
**63. Junhan Kim (2021 winter & spring)
**64. Suyong Choi (2021 winter)
**65. Sujin Pyeon (2021 Spring)
**66. Hyeon Hee Ji (2021 Spring)
**67. Semin Kim (2021 Summer)
**68. Su Hwan Kim (2021 Summer)
**69. Yongbin Kim (2021 Summer)
**70. Nan Park (2021 Summer)
**71. Hoyong Jung (2021 Summer)
**72. Ingyeong Koh (2021 Summer)
**73. Jongbin Jeong (2022 Winter)
**74. Sungchul Yang (2022 Winter, Spring, Summer)
**75. Hyojung Lee (2022 Winter, Spring)
**76. Jun Hyeong Kim (2022 Winter, Spring)
**77. Young Ji Roh (2022 Spring, Summer)
**78. Geon Koh (2022 Spring, Summer)
**79. Hayoung Kang (2022 Summer, 2023 Spring)
**80. Won Jong Kim (2022 Summer, Fall, 2023 Winter)
**81. Christian Lee (2022 Summer)
**82. Je Yun Kang (2022 Summer)
**83. Sumin Lee (2022 Fall)
**84. Jungyeon Kim (2022 Fall, 2023 Winter)
**85. Seol Song (2023 Winter)
**86. Soyeon Kim (2023 Summer)
**87. Sieun Park (2023 Summer)
**88. Gunhyeong Lee (2023 Summer)
**89. Yunseo Han (2023 Summer)
**90. Jae Hyun Kim (2023 Summer)
**91. Jeong-min Seo (2023 Summer)
**92. Yerin Kim (2023 Fall, 2024 Winter)
**93. Sang Min Park (2024 Winter)
**94. Minsun Seo (2024 Winter)
**95. Jaeryun Sim (2024 Winter)
**96. Sun Min Lim (2024 Winter)
**97. Yurim Jung (2024 Spring, Summer)
**98. Hae Been Lee (2024 Spring, Summer)
**99. Zunu An (2024 Summer, Fall, 2025 Winter, Spring, Summer, Fall, 2026 Winter)
**100. Se Bin Lim (2024 Summer, Fall, 2025 Winter)
**101. Sang Min Yoon (2024 Summer)
**102. Yena Kim (2024 Summer)
**103. Kang Eon Lee (2024 Fall)
**104. Soyoon Park (2025 Winter)
**105. Sojung Lee (2025 Winter)
**106. Leanne Ma (2025 Winter)
**107. Seung Wan Jeon (2025 Summer, Fall, 2026 Winter)
**108. Joongun Lee (2025 Summer)
**109. Minseo Kim (2025 Summer)
**110. Hong Kyu Park (2025 Summer)
**111. Yunyeong Jang (2025 Fall, 2026 Winter)
**112. Jong Hyun Hwang (2025 Fall, 2026 Winter)
**113. Gyuweon Park (2025 Fall)
**114. Sung Min Kim (2026 Winter)
**115. Zixuan Guo (2026 Winter)
**116. Hyeonjin Kim (2026 Winter)
**117. Eunjeong Kim (2026 Winter)

People

2026-03-18T06:39:48Z

Il1001: /* Alumni */

__NOTOC__
=='''Scientists & Research Staff'''==
{|border="0" width="1080"
|align="center"|[[File:prof_Insuk_fixed.png|100px|link=people:IS_Lee]]
|align="center"|[[File:SM_fixed.png|100px|link=people:SM_Yang]]
|align="center"|[[File:Ilseok_fixed.png|100px|link=People:IS_Choi]]
|align="center"|[[File:JunHyeong_fixed.png|100px|link=People:Jun_Hyung_Cha]]
|align="center"|[[File:JunYeong_fixed.png|100px|link=People:Junyeong_Ma]]
|align="center"|[[File:Hanjune_fixed.png|100px|link=People:Han-June_KIM]]
|align="center"|[[File:EuiJeong_fixed.png|100px|link=People:EuiJeong_Sung]]
|-

|width=160px; align="center"|[[people:IS_Lee|<big>'''Insuk Lee'''</big>]]
|width=160px; align="center"|[[people:SM_Yang|<big>'''Sunmo Yang'''</big>]]
|width=160px; align="center"|[[People:IS_Choi|<big>'''Ilseok Choi'''</big>]]
|width=160px; align="center"|[[People:Jun_Hyung_Cha|<big>'''Jun Hyung Cha'''</big>]]
|width=160px; align="center"|[[People:Junyeong_Ma|<big>'''Junyeong Ma'''</big>]]
|width=160px; align="center"|[[People:Hanjune_Kim|<big>'''Hanjune Kim'''</big>]]
|width=160px; align="center"|[[People:Euijeong_Sung|<big>'''Euijeong Sung'''</big>]]
|-

|align="center"|[[people:IS_Lee|Principal Investigator Professor]]
|align="center"|[[people:SM_Yang|Bioinformatics Programmer & Sys. Admin]]
|align="center"|[[People:IS_Choi|Ph.D candidate (Single-cell Biology) (2020.9 - )]]
|align="center"|[[People:Jun_Hyung_Cha|Ph.D candidate (Microbiome) (2020.9 - )]]
|align="center"|[[People:Junyeong_Ma|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Hanjune_Kim|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Euijeong_Sung|Ph.D candidate (Single-cell Biology) (2021.9 - )]]
|}
{|border="0" width="1080"

|align="center"|[[File:Sehun_fixed.png|100px|link=People:Sehun_Ahn]]
|align="center"|[[File:Jungyeon_fixed.png|100px|link=People:Jungyeon_Kim]]
|align="center"|[[File:Yerin_fixed.png|100px|link=People:Yerin_Kim]]
|align="center"|[[File:Yurim_fixed_(2).jpg|100px|link=People:Yurim_Jung]]
|align="center"|[[File:HaeBeen_fixed.jpg|100px|link=People:Hae_Been_lee]]
|align="center"|[[File:Sebin_fixed.jpg|100px|link=People:Sebin_Lim]]
|-
|width=160px; align="center"|[[People:Sehun_Ahn|<big>'''Sehun Ahn'''</big>]]
|width=160px; align="center"|[[People:Jungyeon_Kim|<big>'''Jungyeon Kim'''</big>]]
|width=160px; align="center"|[[People:Yerin_Kim|<big>'''Yerin Kim'''</big>]]
|width=160px; align="center"|[[People:Yurim_Jung|<big>'''Yurim Jung'''</big>]]
|width=160px; align="center"|[[People:Hae_Been_lee|<big>'''Hae Been Lee'''</big>]]
|width=160px; align="center"|[[People:Sebin_Lim|<big>'''Sebin Lim'''</big>]]
|-
|align="center"|[[People:Sehun_Ahn|Ph.D candidate (Microbiome) (2022.3 - )]]
|align="center"|[[People:Jungyeon_Kim|Integrated Ph.D candidate (Microbiome) (2023.3 - )]]
|align="center"|[[People:Yerin_Kim|Integrated Ph.D course (Microbiome) (2024.3 - )]]
|align="center"|[[People:Yurim_Jung|Integrated Ph.D course (Single-cell Biology) (2024.9 - )]]
|align="center"|[[People:Hae_Been_lee|Integrated Ph.D course (Microbiome) (2024.9 - )]]
|align="center"|[[People:Sebin_Lim|Integrated Ph.D course (Microbiome) (2025.3 - )]]
|}

=='''Administrative Assistant'''==

=='''Undergraduate Students'''==
*Zunu An
*Seung Wan Jeon
*Yunyeong Jang
*Jong Hyun Hwang
*Sung Min Kim
*Zixuan Guo
*Hyeonjin Kim
*Eunjeong Kim

=='''Alumni'''==
*'''Former Post-docs and Staff Scientists'''
**1. Taeyun Oh (2009.5-2011.12), currently Senior Researcher at Cowellbiogim, Korea
**2. Sohyun Hwang (2010.3-2015.8), currently Professor at [https://grad.cha.ac.kr/%ed%99%a9%ec%86%8c%ed%98%84/ Department of Biomedical Science, CHA University], Korea [https://scholar.google.com/citations?user=z5yC9cwAAAAJ&hl=en Google Scholar] (차의과대학 의과학과 교수)
**3. Samuel Beck (2011.2-2011.12), currently Associate Professor at Boston University, USA, [https://beck310.wixsite.com/becklab Lab Homepage] (미 보스턴 대학교 부교수)
**4. Jawon Song (2011.1-2012.5), currently Research Associate at [https://www.tacc.utexas.edu/about/directory/jawon-song Texas Advanced Computing Center], Austin, TX, USA [https://scholar.google.com/citations?user=wv61wGoAAAAJ&hl=en Google Scholar] (미국 텍사스슈퍼컴퓨팅센터 선임연구원)
**5. Yoonhee Ko (2012.8-2014.2), currently Associate Professor at [https://hufsbiomed.weebly.com/ Department of Biomedical Engineering, Hankuk University of Foreign Studies], Korea [https://scholar.google.com/citations?user=GBxCYX8AAAAJ&hl=en Google Scholar] (한국외국어대 바이오공학과 교수)
**6. Jonghoon Lee (2013.10-2014.2), currently Professor at [https://www.gachon.ac.kr/foodbiotech/6142/subview.do Department of Food Biotechnology, Gachon University], Korea (가천대학교 식품생명공학과 교수)
**7. Jung Eun Shim (2009.8-2017.11), currently Staff Scientist at Yonsei Genomics Center Bioinformatics Data Analysis Core (연세의료원 유전체센터 생명정보분석코어 책임연구원)

*'''Former Graduate Students (Ph.D)'''
**1. Junha Shin (2008.9-2014.2), PhD; currently Scientist at [https://wid.wisc.edu/people/junha-shin/ Wisconsin Institute for Discovery], USA (미국 위스콘신 대학연구소 연구원)
**2. Hanhae Kim (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**3. Ara Cho (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**4. Eiru Kim (2010.9-2016.8), PhD; currently Senior Expert in Data Science, [https://www.gnf.org/ The Genomics Institute of the Novartis Research Foundation], San Diego, USA (노바티스 선임데이터분석연구원)
**5. Tak Lee (2011.3-2017.2), PhD; currently Senior Bioinformatician, [https://www.mpipz.mpg.de/en Max Planck Institute for Plant Breeding Research] (독일 막스플랭크 연구소 선임생명정보학자)
**6. Heonjong Han (2013.3~2019.8), PhD; currently Bioinformatics engineer at [https://3billion.io/ 3billion] (바이오기업 데이터사이언티스트)
**7. Kyungsoo Kim (2013.3~2020.2), PhD; currently Research Professor at Severance Hospital (강남세브란스의료원 유방암센터 연구교수)
**8. Jae-Won Cho (2016.9~2021.2), PhD; currently Assistant Professor at [https://ibb.hanyang.ac.kr/ Hanyang Institute of Bioscience and Biotechnology] (한양대학교 한양생명과학기술원 조교수)
**9. Chan Yeong Kim (2015.3~2021.2), PhD; currently Postdoc Fellow at European Molecular Biology Laboratory in Heidelberg [http://www.bork.embl.de/j/ Bork Group] (유럽연합분자생물학연구소 박사후 연구원)
**10. Sungho Lee (2017.3-2024.2), PhD; currently Data Scientist at [http://www.mogam.re.kr/kor/ MOGAM Institute for Biomedical Research] (목암생명과학연구소, (주)녹십자 출연 연구소, 선임연구원)
**11. Junha Cha (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://dna-discovery.stanford.edu/ Prof. Hanlee P. Ji Lab](미국 스탠퍼드대학교 박사후연구원)
**12. Seungbyn Baek (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://kundajelab.github.io/ Prof. Anshul Kundaje Lab](미국 스탠퍼드대학교 박사후연구원)
**13. Nayeon Kim (2019.9-2025.2), PhD; currently Postdoc Fellow at KAIST InnoCORE Research Group (과학기술원 InnoCORE 초거대언어모델 혁신 연구단, 박사후연구원)
**14. Jun Hyung Cha (2020.3-2026.2), PhD;

*'''Former Graduate Students (Master's degree)'''
**1. Sun-Gou Ji (2009.9-2011.8), M.Eng.; PhD from University of Cambridge (Sanger Genome center); currently Vice President, Computational Genetics at [https://bridgebio.com/ BridgeBio Pharma], Boston, USA (미 바이오기업 부대표)
**2. Hyojin Kim (2013.3-2015.2), M.Eng.; PhD from University of Aachen; currently Scientist at Bayer, Germany [https://www.linkedin.com/in/hyojin-kim-b3bb711ab Linkedin] (독일 바이엘 제약회사 선임 연구원)
**3. Hongseok Shim (2013.9-2015.8), M.Eng.; currently PhD student, Arizona State University, Biomedical Informatics program (애리조나주립대 생물정보학 박사과정)
**4. Sunmo Yang (2014.9-2017.2), M.Eng. currently Bioinformatics programmer, Yonsei University (연세대 네트워크생명공학 연구실 책임데이터연구원)
**5. Muyoung Lee (2016.3-2018.2), M.Eng. currently PhD student, University of Texas at Austin, Cellular and Molecular Biology Program (텍사스주립대 생물정보학 박사과정)
**6. Jiwon Yu (2021.9-2023.8), M.Eng. currently Data Scientist at [https://www.samsungbioepis.com/kr/index.do SAMSUNG BIOEPIS] (삼성바이오에피스 데이터사이언티스트)
**7. Geon_Koh (2022.9-2025.2), M.Eng. currently Researcher at Gachon University, College of Medicine (가천의대 시스템생물학 연구실 연구원)
**8. Wonjong Kim (2023.3-2025.8), M.Eng. currently Researcher at [https://samsungbiologics.com/ SAMSUNG Biologics] (삼성바이오로직스 연구원)

*'''Former Visiting Scientists/Students'''
**1. Minkyung Shin (2012.3-2012.7), went to University of Southern California graduate school
**2. Paul Chung (2012 summer), currently work at [https://about.meta.com/ Meta], USA
**3. Hyunjin Cho (2014 summer), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA
**4. Michael Chung (2016.8-2016.12), currently work at [https://about.meta.com/ Meta], USA

*'''Former Undergraduate Students'''
**1. Ila Shin, went to medical school (Yonsei Univ.) Currently Professor, Kyunghee University School of Medicine (경희대학교 의과대학 교수)
**2. Yoonkyung Ko
**3. Sangyo Park, went to law school (Kyounghee Univ.)
**4. Jayoon Shin, went to medical school (Pusan National Univ.)
**5. Dongjoo Sun, went to dental school (Wongwang Univ.)
**6. Eulsoo Kim
**7. Myungwhan Lee, went to medical school (Yonsei Univ.)
**8. Moonhee Lee, went to graduate school (University of Amsterdam, Netherlands)
**9. Jinhyun Ju, went to graduate school (Cornell Medical School, Computational Systems Biology); Currently Principal Computational Biologist, Cancer Genomics at [https://bridgebio.com/ BridgeBio Pharma], Seattle, USA (미 바이오기업 선임연구원)
**10. Haeyoung Shin, went to graduate school (Brown University, Computational Neuroscience); Currently Professor, Seoul National University (서울대학교 생명과학부 교수)
**11. Joonghee Soh, went to graduate school (KAIST, Culture Technology)
**12. Hee Jung Cho, went to graduate school (UC Berkeley)
**13. TaeHwan Kim, went to medical school
**14. Joohyung Kim, went to medical school (Kyungpook National Univ.)
**15. Donghyun Shin, went to medical school (Yonsei Univ.)
**16. Byunghee Kang (2015 spring - 2016 summer), went to graduate school (PosTech)
**17. Sunphil Kim (2016 winter)
**18. Jaeho Shim (2016 winter)
**19. Seunghyun Shin (2016 spring)
**20. Aejoo Hong (2016 spring)
**21. Changbae Bang (2016 summer), went to medical school (Yonsei Univ.)
**22. Seoyoung Choi (2016 summer)
**23. Dabin Jung (2016 summer)
**24. Boreum Nam (2016 summer)
**25. Seungun Lee (2016 summer)
**26. Yeaji Kim (2016 summer and fall)
**27. Sangyoung Lee (2017 winter)
**28. Heejun Jang (2017 winter & spring), went to KIST as Research Assistant
**29. Jungha Lee (2017 summer), went to graduate school (Seoul National Univ.)
**30. Seunghyun Wang (2017 summer), went to graduate school (KAIST)
**31. Dong-Min Yang (2017 fall)
**32. Doo-Hee Lee (2017 fall)
**33. Suk-Jae Han (2018 winter)
**34. Ji-Eun Han (2018 winter)
**35. Yuri Ko (2018 spring)
**36. Sung-Woo Kim (2018 spring)
**37. Woosung Kwon (2018 summer)
**38. Soyun Kong (2018 summer)
**39. Hojeong Keum (2018 summer and fall)
**40. Sungjun Lim (2018 summer and fall)
**41. Jiyoon Lee (2018 summer and fall)
**42. Ilseok Choi(2019 winter, spring, summer and fall, 2020 winter, spring)
**43. Junik Park (2019 winter)
**44. Lee Yoo (2019 winter & spring)
**45. Yeonwha Kim (2019 winter & spring)
**46. Sohee Kim (2019 spring)
**47. Juseong Lee (2019 spring)
**48. Junyoung Yang (2019 spring & summer)
**49. Junyeong Ma (2019 summer, 2020 winter, summer, fall, 2021 winter)
**50. Dayeon Jung (2019 summer)
**51. Hanjoon Kim (2019 summer, 2021 winter)
**52. Hyungjin Kim (2020 winter, spring)
**53. Sujin Hyun (2020 winter)
**54. Hyuki Lee (2020 winter)
**55. Donghwan Lee (2020 winter)
**56. Jun Hyung Cha (2020 spring, summer)
**57. Jiwon Yu (2020 summer, 2021 Spring, summer)
**58. Dong Seok Kim (2020 summer)
**59. Donggeun Lee (2020 summer)
**60. Sehun Ahn (2020 summer, 2021 winter, spring, summer, 2022 winter)
**61. Jiho Kim (2020 summer)
**62. Euijung Seong (2020 fall, 2021 spring, summer)
**63. Junhan Kim (2021 winter & spring)
**64. Suyong Choi (2021 winter)
**65. Sujin Pyeon (2021 Spring)
**66. Hyeon Hee Ji (2021 Spring)
**67. Semin Kim (2021 Summer)
**68. Su Hwan Kim (2021 Summer)
**69. Yongbin Kim (2021 Summer)
**70. Nan Park (2021 Summer)
**71. Hoyong Jung (2021 Summer)
**72. Ingyeong Koh (2021 Summer)
**73. Jongbin Jeong (2022 Winter)
**74. Sungchul Yang (2022 Winter, Spring, Summer)
**75. Hyojung Lee (2022 Winter, Spring)
**76. Jun Hyeong Kim (2022 Winter, Spring)
**77. Young Ji Roh (2022 Spring, Summer)
**78. Geon Koh (2022 Spring, Summer)
**79. Hayoung Kang (2022 Summer, 2023 Spring)
**80. Won Jong Kim (2022 Summer, Fall, 2023 Winter)
**81. Christian Lee (2022 Summer)
**82. Je Yun Kang (2022 Summer)
**83. Sumin Lee (2022 Fall)
**84. Jungyeon Kim (2022 Fall, 2023 Winter)
**85. Seol Song (2023 Winter)
**86. Soyeon Kim (2023 Summer)
**87. Sieun Park (2023 Summer)
**88. Gunhyeong Lee (2023 Summer)
**89. Yunseo Han (2023 Summer)
**90. Jae Hyun Kim (2023 Summer)
**91. Jeong-min Seo (2023 Summer)
**92. Yerin Kim (2023 Fall, 2024 Winter)
**93. Sang Min Park (2024 Winter)
**94. Minsun Seo (2024 Winter)
**95. Jaeryun Sim (2024 Winter)
**96. Sun Min Lim (2024 Winter)
**97. Yurim Jung (2024 Spring, Summer)
**98. Hae Been Lee (2024 Spring, Summer)
**99. Zunu An (2024 Summer, Fall, 2025 Winter, Spring, Summer, Fall, 2026 Winter)
**100. Se Bin Lim (2024 Summer, Fall, 2025 Winter)
**101. Sang Min Yoon (2024 Summer)
**102. Yena Kim (2024 Summer)
**103. Kang Eon Lee (2024 Fall)
**104. Soyoon Park (2025 Winter)
**105. Sojung Lee (2025 Winter)
**106. Leanne Ma (2025 Winter)
**107. Seung Wan Jeon (2025 Summer, Fall, 2026 Winter)
**108. Joongun Lee (2025 Summer)
**109. Minseo Kim (2025 Summer)
**110. Hong Kyu Park (2025 Summer)
**111. Yunyeong Jang (2025 Fall, 2026 Winter)
**112. Jong Hyun Hwang (2025 Fall, 2026 Winter)
**113. Gyuweon Park (2025 Fall)
**114. Sung Min Kim (2026 Winter)
**115. Zixuan Guo (2026 Winter)
**116. Hyeonjin Kim (2026 Winter)
**117. Eunjeong Kim (2026 Winter)

Publications

2026-03-18T06:33:41Z

Il1001: /* 2026 (8) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (8)==
*134. Metformin beyond Glycemic Control: New Mechanistic Insights and Expanding Therapeutic Horizons, '''''Under Review'''''
 
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Under Review'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Revision'''''
 
*131. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*130. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*129. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Nature Communications''''' Accepted
 
*128. '''Jun Hyung Cha*, Sol-Ah Jeong*''', Byoung-Seok Ye, '''Insuk Lee**, Bock-Young**''', Jung Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia, '''''Journal of Oral Microbiology''''' 2026 Mar 11;18(1):2643036 [https://pubmed.ncbi.nlm.nih.gov/41836788/ pubmed]
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [//pubmed.gov/36289209 PubMed] [//www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [//pubmed.gov/36291657 PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [//pubmed.gov/36057640 PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [//pubmed.gov/35672321 PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [//pubmed.gov/34987166 PubMed] [//netbiolab.org/wiki/files/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [//pubmed.gov/34747468 PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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] [//netbiolab.org/wiki/files/glucose_germrate.txt Supplementary File 1] [//netbiolab.org/wiki/files/glucose_sig_accessions.txt Supplementary File 2]
 

==2020 (9)==
*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]
 
*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]
 
*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 [//netbiolab.org/wiki/files/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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2026-03-18T06:33:21Z

Il1001: /* 2026 (7) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (8)==
*134. Metformin beyond Glycemic Control: New Mechanistic Insights and Expanding Therapeutic Horizons, '''''Under Revision'''''
 
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Under Review'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Revision'''''
 
*131. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*130. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*129. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Nature Communications''''' Accepted
 
*128. '''Jun Hyung Cha*, Sol-Ah Jeong*''', Byoung-Seok Ye, '''Insuk Lee**, Bock-Young**''', Jung Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia, '''''Journal of Oral Microbiology''''' 2026 Mar 11;18(1):2643036 [https://pubmed.ncbi.nlm.nih.gov/41836788/ pubmed]
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [//pubmed.gov/36289209 PubMed] [//www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [//pubmed.gov/36291657 PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [//pubmed.gov/36057640 PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [//pubmed.gov/35672321 PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [//pubmed.gov/34987166 PubMed] [//netbiolab.org/wiki/files/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [//pubmed.gov/34747468 PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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] [//netbiolab.org/wiki/files/glucose_germrate.txt Supplementary File 1] [//netbiolab.org/wiki/files/glucose_sig_accessions.txt Supplementary File 2]
 

==2020 (9)==
*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]
 
*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]
 
*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 [//netbiolab.org/wiki/files/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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2026-03-18T06:29:00Z

Il1001: /* 2026 (7) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (7)==
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Under Review'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Revision'''''
 
*131. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*130. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*129. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Nature Communications''''' Accepted
 
*128. '''Jun Hyung Cha*, Sol-Ah Jeong*''', Byoung-Seok Ye, '''Insuk Lee**, Bock-Young**''', Jung Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia, '''''Journal of Oral Microbiology''''' 2026 Mar 11;18(1):2643036 [https://pubmed.ncbi.nlm.nih.gov/41836788/ pubmed]
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [//pubmed.gov/36289209 PubMed] [//www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [//pubmed.gov/36291657 PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [//pubmed.gov/36057640 PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [//pubmed.gov/35672321 PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [//pubmed.gov/34987166 PubMed] [//netbiolab.org/wiki/files/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [//pubmed.gov/34747468 PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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] [//netbiolab.org/wiki/files/glucose_germrate.txt Supplementary File 1] [//netbiolab.org/wiki/files/glucose_sig_accessions.txt Supplementary File 2]
 

==2020 (9)==
*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]
 
*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]
 
*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 [//netbiolab.org/wiki/files/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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2026-03-18T06:25:28Z

Il1001: /* 2026 (7) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (7)==
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Under Review'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Revision'''''
 
*131. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*130. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*129. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Nature Communications''''' Accepted
 
*128. Jun Hyung Cha 1, Sol-Ah Jeong 2, Byoung-Seok Ye 3, Insuk Lee 1 4, Bock-Young Jung Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Journal of Oral Microbiology''''' In press
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [//pubmed.gov/36289209 PubMed] [//www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [//pubmed.gov/36291657 PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [//pubmed.gov/36057640 PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [//pubmed.gov/35672321 PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [//pubmed.gov/34987166 PubMed] [//netbiolab.org/wiki/files/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [//pubmed.gov/34747468 PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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] [//netbiolab.org/wiki/files/glucose_germrate.txt Supplementary File 1] [//netbiolab.org/wiki/files/glucose_sig_accessions.txt Supplementary File 2]
 

==2020 (9)==
*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]
 
*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]
 
*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 [//netbiolab.org/wiki/files/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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2026-03-18T06:24:45Z

Il1001: /* 2026 (7) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (7)==
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Under Review'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Revision'''''
 
*131. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*130. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*129. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Nature Communications''''' Accepted
 
*128. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Journal of Oral Microbiology''''' In press
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [//pubmed.gov/36289209 PubMed] [//www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [//pubmed.gov/36291657 PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [//pubmed.gov/36057640 PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [//pubmed.gov/35672321 PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [//pubmed.gov/34987166 PubMed] [//netbiolab.org/wiki/files/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [//pubmed.gov/34747468 PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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] [//netbiolab.org/wiki/files/glucose_germrate.txt Supplementary File 1] [//netbiolab.org/wiki/files/glucose_sig_accessions.txt Supplementary File 2]
 

==2020 (9)==
*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]
 
*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]
 
*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 [//netbiolab.org/wiki/files/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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2026-03-07T06:19:58Z

Il1001: /* 2026 (7) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (7)==
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Under Review'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Review'''''
 
*131. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Journal of Oral Microbiology''''' In press
 
*130. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*128. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Nature Communications''''' Accepted
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [//pubmed.gov/36289209 PubMed] [//www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [//pubmed.gov/36291657 PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [//pubmed.gov/36057640 PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [//pubmed.gov/35672321 PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [//pubmed.gov/34987166 PubMed] [//netbiolab.org/wiki/files/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [//pubmed.gov/34747468 PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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] [//netbiolab.org/wiki/files/glucose_germrate.txt Supplementary File 1] [//netbiolab.org/wiki/files/glucose_sig_accessions.txt Supplementary File 2]
 

==2020 (9)==
*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]
 
*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]
 
*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 [//netbiolab.org/wiki/files/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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

People

2026-02-27T05:59:38Z

Il1001:

__NOTOC__
=='''Scientists & Research Staff'''==
{|border="0" width="1080"
|align="center"|[[File:prof_Insuk_fixed.png|100px|link=people:IS_Lee]]
|align="center"|[[File:SM_fixed.png|100px|link=people:SM_Yang]]
|align="center"|[[File:Ilseok_fixed.png|100px|link=People:IS_Choi]]
|align="center"|[[File:JunHyeong_fixed.png|100px|link=People:Jun_Hyung_Cha]]
|align="center"|[[File:JunYeong_fixed.png|100px|link=People:Junyeong_Ma]]
|align="center"|[[File:Hanjune_fixed.png|100px|link=People:Han-June_KIM]]
|align="center"|[[File:EuiJeong_fixed.png|100px|link=People:EuiJeong_Sung]]
|-

|width=160px; align="center"|[[people:IS_Lee|<big>'''Insuk Lee'''</big>]]
|width=160px; align="center"|[[people:SM_Yang|<big>'''Sunmo Yang'''</big>]]
|width=160px; align="center"|[[People:IS_Choi|<big>'''Ilseok Choi'''</big>]]
|width=160px; align="center"|[[People:Jun_Hyung_Cha|<big>'''Jun Hyung Cha'''</big>]]
|width=160px; align="center"|[[People:Junyeong_Ma|<big>'''Junyeong Ma'''</big>]]
|width=160px; align="center"|[[People:Hanjune_Kim|<big>'''Hanjune Kim'''</big>]]
|width=160px; align="center"|[[People:Euijeong_Sung|<big>'''Euijeong Sung'''</big>]]
|-

|align="center"|[[people:IS_Lee|Principal Investigator Professor]]
|align="center"|[[people:SM_Yang|Bioinformatics Programmer & Sys. Admin]]
|align="center"|[[People:IS_Choi|Ph.D candidate (Single-cell Biology) (2020.9 - )]]
|align="center"|[[People:Jun_Hyung_Cha|Ph.D candidate (Microbiome) (2020.9 - )]]
|align="center"|[[People:Junyeong_Ma|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Hanjune_Kim|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Euijeong_Sung|Ph.D candidate (Single-cell Biology) (2021.9 - )]]
|}
{|border="0" width="1080"

|align="center"|[[File:Sehun_fixed.png|100px|link=People:Sehun_Ahn]]
|align="center"|[[File:Jungyeon_fixed.png|100px|link=People:Jungyeon_Kim]]
|align="center"|[[File:Yerin_fixed.png|100px|link=People:Yerin_Kim]]
|align="center"|[[File:Yurim_fixed_(2).jpg|100px|link=People:Yurim_Jung]]
|align="center"|[[File:HaeBeen_fixed.jpg|100px|link=People:Hae_Been_lee]]
|align="center"|[[File:Sebin_fixed.jpg|100px|link=People:Sebin_Lim]]
|-
|width=160px; align="center"|[[People:Sehun_Ahn|<big>'''Sehun Ahn'''</big>]]
|width=160px; align="center"|[[People:Jungyeon_Kim|<big>'''Jungyeon Kim'''</big>]]
|width=160px; align="center"|[[People:Yerin_Kim|<big>'''Yerin Kim'''</big>]]
|width=160px; align="center"|[[People:Yurim_Jung|<big>'''Yurim Jung'''</big>]]
|width=160px; align="center"|[[People:Hae_Been_lee|<big>'''Hae Been Lee'''</big>]]
|width=160px; align="center"|[[People:Sebin_Lim|<big>'''Sebin Lim'''</big>]]
|-
|align="center"|[[People:Sehun_Ahn|Ph.D candidate (Microbiome) (2022.3 - )]]
|align="center"|[[People:Jungyeon_Kim|Integrated Ph.D candidate (Microbiome) (2023.3 - )]]
|align="center"|[[People:Yerin_Kim|Integrated Ph.D course (Microbiome) (2024.3 - )]]
|align="center"|[[People:Yurim_Jung|Integrated Ph.D course (Single-cell Biology) (2024.9 - )]]
|align="center"|[[People:Hae_Been_lee|Integrated Ph.D course (Microbiome) (2024.9 - )]]
|align="center"|[[People:Sebin_Lim|Integrated Ph.D course (Microbiome) (2025.3 - )]]
|}

=='''Administrative Assistant'''==

=='''Undergraduate Students'''==
*Zunu An
*Seung Wan Jeon
*Yunyeong Jang
*Jong Hyun Hwang
*Sung Min Kim
*Zixuan Guo
*Hyeonjin Kim
*Eunjeong Kim

=='''Alumni'''==
*'''Former Post-docs and Staff Scientists'''
**1. Taeyun Oh (2009.5-2011.12), currently Senior Researcher at Cowellbiogim, Korea
**2. Sohyun Hwang (2010.3-2015.8), currently Professor at [https://grad.cha.ac.kr/%ed%99%a9%ec%86%8c%ed%98%84/ Department of Biomedical Science, CHA University], Korea [https://scholar.google.com/citations?user=z5yC9cwAAAAJ&hl=en Google Scholar] (차의과대학 의과학과 교수)
**3. Samuel Beck (2011.2-2011.12), currently Associate Professor at Boston University, USA, [https://beck310.wixsite.com/becklab Lab Homepage] (미 보스턴 대학교 부교수)
**4. Jawon Song (2011.1-2012.5), currently Research Associate at [https://www.tacc.utexas.edu/about/directory/jawon-song Texas Advanced Computing Center], Austin, TX, USA [https://scholar.google.com/citations?user=wv61wGoAAAAJ&hl=en Google Scholar] (미국 텍사스슈퍼컴퓨팅센터 선임연구원)
**5. Yoonhee Ko (2012.8-2014.2), currently Associate Professor at [https://hufsbiomed.weebly.com/ Department of Biomedical Engineering, Hankuk University of Foreign Studies], Korea [https://scholar.google.com/citations?user=GBxCYX8AAAAJ&hl=en Google Scholar] (한국외국어대 바이오공학과 교수)
**6. Jonghoon Lee (2013.10-2014.2), currently Professor at [https://www.gachon.ac.kr/foodbiotech/6142/subview.do Department of Food Biotechnology, Gachon University], Korea (가천대학교 식품생명공학과 교수)
**7. Jung Eun Shim (2009.8-2017.11), currently Staff Scientist at Yonsei Genomics Center Bioinformatics Data Analysis Core (연세의료원 유전체센터 생명정보분석코어 책임연구원)

*'''Former Graduate Students (Ph.D)'''
**1. Junha Shin (2008.9-2014.2), PhD; currently Scientist at [https://wid.wisc.edu/people/junha-shin/ Wisconsin Institute for Discovery], USA (미국 위스콘신 대학연구소 연구원)
**2. Hanhae Kim (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**3. Ara Cho (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**4. Eiru Kim (2010.9-2016.8), PhD; currently Senior Expert in Data Science, [https://www.gnf.org/ The Genomics Institute of the Novartis Research Foundation], San Diego, USA (노바티스 선임데이터분석연구원)
**5. Tak Lee (2011.3-2017.2), PhD; currently Senior Bioinformatician, [https://www.mpipz.mpg.de/en Max Planck Institute for Plant Breeding Research] (독일 막스플랭크 연구소 선임생명정보학자)
**6. Heonjong Han (2013.3~2019.8), PhD; currently Bioinformatics engineer at [https://3billion.io/ 3billion] (바이오기업 데이터사이언티스트)
**7. Kyungsoo Kim (2013.3~2020.2), PhD; currently Research Professor at Severance Hospital (강남세브란스의료원 유방암센터 연구교수)
**8. Jae-Won Cho (2016.9~2021.2), PhD; currently Assistant Professor at [https://ibb.hanyang.ac.kr/ Hanyang Institute of Bioscience and Biotechnology] (한양대학교 한양생명과학기술원 조교수)
**9. Chan Yeong Kim (2015.3~2021.2), PhD; currently Postdoc Fellow at European Molecular Biology Laboratory in Heidelberg [http://www.bork.embl.de/j/ Bork Group] (유럽연합분자생물학연구소 박사후 연구원)
**10. Sungho Lee (2017.3-2024.2), PhD; currently Data Scientist at [http://www.mogam.re.kr/kor/ MOGAM Institute for Biomedical Research] (목암생명과학연구소, (주)녹십자 출연 연구소, 선임연구원)
**11. Junha Cha (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://dna-discovery.stanford.edu/ Prof. Hanlee P. Ji Lab](미국 스탠퍼드대학교 박사후연구원)
**12. Seungbyn Baek (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://kundajelab.github.io/ Prof. Anshul Kundaje Lab](미국 스탠퍼드대학교 박사후연구원)
**13. Nayeon Kim (2019.9-2025.2), PhD; currently Postdoc Fellow at KAIST InnoCORE Research Group (과학기술원 InnoCORE 초거대언어모델 혁신 연구단, 박사후연구원)

*'''Former Graduate Students (Master's degree)'''
**1. Sun-Gou Ji (2009.9-2011.8), M.Eng.; PhD from University of Cambridge (Sanger Genome center); currently Vice President, Computational Genetics at [https://bridgebio.com/ BridgeBio Pharma], Boston, USA (미 바이오기업 부대표)
**2. Hyojin Kim (2013.3-2015.2), M.Eng.; PhD from University of Aachen; currently Scientist at Bayer, Germany [https://www.linkedin.com/in/hyojin-kim-b3bb711ab Linkedin] (독일 바이엘 제약회사 선임 연구원)
**3. Hongseok Shim (2013.9-2015.8), M.Eng.; currently PhD student, Arizona State University, Biomedical Informatics program (애리조나주립대 생물정보학 박사과정)
**4. Sunmo Yang (2014.9-2017.2), M.Eng. currently Bioinformatics programmer, Yonsei University (연세대 네트워크생명공학 연구실 책임데이터연구원)
**5. Muyoung Lee (2016.3-2018.2), M.Eng. currently PhD student, University of Texas at Austin, Cellular and Molecular Biology Program (텍사스주립대 생물정보학 박사과정)
**6. Jiwon Yu (2021.9-2023.8), M.Eng. currently Data Scientist at [https://www.samsungbioepis.com/kr/index.do SAMSUNG BIOEPIS] (삼성바이오에피스 데이터사이언티스트)
**7. Geon_Koh (2022.9-2025.2), M.Eng. currently Researcher at Gachon University, College of Medicine (가천의대 시스템생물학 연구실 연구원)
**8. Wonjong Kim (2023.3-2025.8), M.Eng. currently Researcher at [https://samsungbiologics.com/ SAMSUNG Biologics] (삼성바이오로직스 연구원)

*'''Former Visiting Scientists/Students'''
**1. Minkyung Shin (2012.3-2012.7), went to University of Southern California graduate school
**2. Paul Chung (2012 summer), currently work at [https://about.meta.com/ Meta], USA
**3. Hyunjin Cho (2014 summer), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA
**4. Michael Chung (2016.8-2016.12), currently work at [https://about.meta.com/ Meta], USA

*'''Former Undergraduate Students'''
**1. Ila Shin, went to medical school (Yonsei Univ.) Currently Professor, Kyunghee University School of Medicine (경희대학교 의과대학 교수)
**2. Yoonkyung Ko
**3. Sangyo Park, went to law school (Kyounghee Univ.)
**4. Jayoon Shin, went to medical school (Pusan National Univ.)
**5. Dongjoo Sun, went to dental school (Wongwang Univ.)
**6. Eulsoo Kim
**7. Myungwhan Lee, went to medical school (Yonsei Univ.)
**8. Moonhee Lee, went to graduate school (University of Amsterdam, Netherlands)
**9. Jinhyun Ju, went to graduate school (Cornell Medical School, Computational Systems Biology); Currently Principal Computational Biologist, Cancer Genomics at [https://bridgebio.com/ BridgeBio Pharma], Seattle, USA (미 바이오기업 선임연구원)
**10. Haeyoung Shin, went to graduate school (Brown University, Computational Neuroscience); Currently Professor, Seoul National University (서울대학교 생명과학부 교수)
**11. Joonghee Soh, went to graduate school (KAIST, Culture Technology)
**12. Hee Jung Cho, went to graduate school (UC Berkeley)
**13. TaeHwan Kim, went to medical school
**14. Joohyung Kim, went to medical school (Kyungpook National Univ.)
**15. Donghyun Shin, went to medical school (Yonsei Univ.)
**16. Byunghee Kang (2015 spring - 2016 summer), went to graduate school (PosTech)
**17. Sunphil Kim (2016 winter)
**18. Jaeho Shim (2016 winter)
**19. Seunghyun Shin (2016 spring)
**20. Aejoo Hong (2016 spring)
**21. Changbae Bang (2016 summer), went to medical school (Yonsei Univ.)
**22. Seoyoung Choi (2016 summer)
**23. Dabin Jung (2016 summer)
**24. Boreum Nam (2016 summer)
**25. Seungun Lee (2016 summer)
**26. Yeaji Kim (2016 summer and fall)
**27. Sangyoung Lee (2017 winter)
**28. Heejun Jang (2017 winter & spring), went to KIST as Research Assistant
**29. Jungha Lee (2017 summer), went to graduate school (Seoul National Univ.)
**30. Seunghyun Wang (2017 summer), went to graduate school (KAIST)
**31. Dong-Min Yang (2017 fall)
**32. Doo-Hee Lee (2017 fall)
**33. Suk-Jae Han (2018 winter)
**34. Ji-Eun Han (2018 winter)
**35. Yuri Ko (2018 spring)
**36. Sung-Woo Kim (2018 spring)
**37. Woosung Kwon (2018 summer)
**38. Soyun Kong (2018 summer)
**39. Hojeong Keum (2018 summer and fall)
**40. Sungjun Lim (2018 summer and fall)
**41. Jiyoon Lee (2018 summer and fall)
**42. Ilseok Choi(2019 winter, spring, summer and fall, 2020 winter, spring)
**43. Junik Park (2019 winter)
**44. Lee Yoo (2019 winter & spring)
**45. Yeonwha Kim (2019 winter & spring)
**46. Sohee Kim (2019 spring)
**47. Juseong Lee (2019 spring)
**48. Junyoung Yang (2019 spring & summer)
**49. Junyeong Ma (2019 summer, 2020 winter, summer, fall, 2021 winter)
**50. Dayeon Jung (2019 summer)
**51. Hanjoon Kim (2019 summer, 2021 winter)
**52. Hyungjin Kim (2020 winter, spring)
**53. Sujin Hyun (2020 winter)
**54. Hyuki Lee (2020 winter)
**55. Donghwan Lee (2020 winter)
**56. Jun Hyung Cha (2020 spring, summer)
**57. Jiwon Yu (2020 summer, 2021 Spring, summer)
**58. Dong Seok Kim (2020 summer)
**59. Donggeun Lee (2020 summer)
**60. Sehun Ahn (2020 summer, 2021 winter, spring, summer, 2022 winter)
**61. Jiho Kim (2020 summer)
**62. Euijung Seong (2020 fall, 2021 spring, summer)
**63. Junhan Kim (2021 winter & spring)
**64. Suyong Choi (2021 winter)
**65. Sujin Pyeon (2021 Spring)
**66. Hyeon Hee Ji (2021 Spring)
**67. Semin Kim (2021 Summer)
**68. Su Hwan Kim (2021 Summer)
**69. Yongbin Kim (2021 Summer)
**70. Nan Park (2021 Summer)
**71. Hoyong Jung (2021 Summer)
**72. Ingyeong Koh (2021 Summer)
**73. Jongbin Jeong (2022 Winter)
**74. Sungchul Yang (2022 Winter, Spring, Summer)
**75. Hyojung Lee (2022 Winter, Spring)
**76. Jun Hyeong Kim (2022 Winter, Spring)
**77. Young Ji Roh (2022 Spring, Summer)
**78. Geon Koh (2022 Spring, Summer)
**79. Hayoung Kang (2022 Summer, 2023 Spring)
**80. Won Jong Kim (2022 Summer, Fall, 2023 Winter)
**81. Christian Lee (2022 Summer)
**82. Je Yun Kang (2022 Summer)
**83. Sumin Lee (2022 Fall)
**84. Jungyeon Kim (2022 Fall, 2023 Winter)
**85. Seol Song (2023 Winter)
**86. Soyeon Kim (2023 Summer)
**87. Sieun Park (2023 Summer)
**88. Gunhyeong Lee (2023 Summer)
**89. Yunseo Han (2023 Summer)
**90. Jae Hyun Kim (2023 Summer)
**91. Jeong-min Seo (2023 Summer)
**92. Yerin Kim (2023 Fall, 2024 Winter)
**93. Sang Min Park (2024 Winter)
**94. Minsun Seo (2024 Winter)
**95. Jaeryun Sim (2024 Winter)
**96. Sun Min Lim (2024 Winter)
**97. Yurim Jung (2024 Spring, Summer)
**98. Hae Been Lee (2024 Spring, Summer)
**99. Zunu An (2024 Summer, Fall, 2025 Winter, Spring, Summer, Fall, 2026 Winter)
**100. Se Bin Lim (2024 Summer, Fall, 2025 Winter)
**101. Sang Min Yoon (2024 Summer)
**102. Yena Kim (2024 Summer)
**103. Kang Eon Lee (2024 Fall)
**104. Soyoon Park (2025 Winter)
**105. Sojung Lee (2025 Winter)
**106. Leanne Ma (2025 Winter)
**107. Seung Wan Jeon (2025 Summer, Fall, 2026 Winter)
**108. Joongun Lee (2025 Summer)
**109. Minseo Kim (2025 Summer)
**110. Hong Kyu Park (2025 Summer)
**111. Yunyeong Jang (2025 Fall, 2026 Winter)
**112. Jong Hyun Hwang (2025 Fall, 2026 Winter)
**113. Gyuweon Park (2025 Fall)
**114. Sung Min Kim (2026 Winter)
**115. Zixuan Guo (2026 Winter)
**116. Hyeonjin Kim (2026 Winter)
**117. Eunjeong Kim (2026 Winter)

Publications

2026-02-26T23:44:21Z

Il1001: /* 2026 (7) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (7)==
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Under Review'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Review'''''
 
*131. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Revision'''''
 
*130. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*128. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Nature Communications''''' Accepted
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2026-02-25T14:03:03Z

Il1001: /* 2026 (7) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (7)==
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Submitted'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Review'''''
 
*131. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Revision'''''
 
*130. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Revision'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*128. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2026-02-25T14:02:05Z

Il1001: /* 2026 (6) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (7)==
*133. LoGoBERT-PPI enables fast and accurate protein–protein interaction mapping at scale '''''Submitted'''''
 
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Review'''''
 
*131. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Revision'''''
 
*130. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Review'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*128. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Software

2026-02-24T04:38:15Z

Il1001: /* CODE and DATABASE in Central Repositories */

__NOTOC__
=='''CODE and DATABASE in Central Repositories'''==
*[https://github.com/netbiolab Netbiolab GitHub site]
*[https://huggingface.co/netbiolab Netbiolab HuggingFace site]

=='''Microbiome Research'''==
[[File:Hrgm logo.png|150px|link=//www.decodebiome.org/HRGM]]
'''HRGM''': A Human Reference Gut Microbiome comprising 232,098 genomes for 5414 prokaryotic species and 103 million unique proteins

[[File:HROM_logo.png|150px|link=//www.decodebiome.org/HROM]]
'''HROM''': A Human Reference Oral Microbiome comprising 72,641 genomes for 3,426 prokaryotic species and 8.49 million unique proteins

[[File:mrgm_logo.png|150px|link=//www.decodebiome.org/MRGM]]
'''MRGM''': A Mouse Reference Gut Microbiome comprising 46,267 genomes for 1,689 bacterial species and 15.2 million proteins

[[File:Mrgv_logo_ad.png|150px|link=//www.decodebiome.org/MRGV]]
'''MRGV''': A Mouse Reference Gut Virome comprising 109,778 genomes for 28,824 species-level vOTUs and 1.3 million unique proteins

=='''Single-cell Biology'''==
[[File:ScHumanNet github banner.final.jpg|150px|link=https://github.com/netbiolab/scHumanNet]]
'''scHumanNet''': Cell-type-specific functional gene networks using single-cell RNA-sequencing data

[[File:VC_logo.png|150px|link=//www.grnpedia.org/cytometry]]
'''VirtualCytometry''': A webserver for the study of immune cell differentiation using single-cell RNA sequencing data.''

=='''Network Medicine'''==
[[File:HumanNet_logo_with_title.png|150px|link=//www.inetbio.org/humannet]]'''HumanNet''': Human gene networks for disease research

[[File:TRRUST_logo.jpg |150px|link=//www.grnpedia.org/trrust/]] '''TRRUST''': Curated TF-target interaction networks in human and mouse

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

[[File:Ngsea logo1.png |150px|link=//www.inetbio.org/ngsea/]] '''NGSEA''': Network-augmented gene set enrichment analysis tool

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

[[File:GWAB_logo.png |150px|link=//www.inetbio.org/gwab]] '''GWAB''': A web server for network-based boosting of human genome-wide association data

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

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

=='''Functional Gene Networks'''==

==''Animals''==
{|border="0" width="400"
|align="center"|[[file:MouseNetLogo.png|150px|link=//www.inetbio.org/mousenet]]
|align="center"|[[file:danionet_logo.png|150px|link=//www.inetbio.org/danionet]]
|align="center"|[[file:Flynet.png|150px|link=//www.inetbio.org/flynet]]
|align="center"|[[file:WormNetv3.jpg|150px|link=//www.inetbio.org/wormnet]]
|-
|align="center"|''Mus musculus''
|align="center"|''Danio rerio''
|align="center"|''Drosophila melanogaster''
|align="center"|''Caenorhabditis elegans''
|}

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

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

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

==''Build your own Functional gene networks''==
[[File:BiomeNet_logo.png | 150px | link=http://kobic.re.kr/biomenet]]
'''BiomeNet''': A database for construction and analysis of functional interaction networks for any species with a sequenced genome

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

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

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

People:IS Lee

2026-02-20T07:20:58Z

Il1001: /* Professional Experience */

__NOTOC__
{|
|[[File:insuklee_fixed.jpg|240px]]
|
===Insuk Lee===
*[https://systemsbiology.yonsei.ac.kr/faculty/member.do?mode=view&userId=098A2bOKAr5Dnt%2B64UrHGg%3D%3D&sosokcd=1010495 Yonsei University Faculty Information]
*Department of Biotechnology
*50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
*Science Research Center S323 (Lab) S328 (Office)
*Office: +82-2-2123-5559
*Email: insuklee(at)yonsei(dot)ac(dot)kr

==Education==
*'''Postdoctoral training, Bioinformatics and Systems Biology''', University of Texas at Austin, TX (01/2003 – 12/2005)
*'''Ph.D., Microbiology''', University of Texas at Austin, TX (09/1996 – 12/2002)
*'''M.S., Biology''', Western Illinois University, Macomb, IL (09/1993 – 05/1996)
*'''B.S., Biology''', Hanyang University, Seoul, Korea (03/1986 – 02/1993, military service: 02/1988 – 05/1990)
|-
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==Awards and Honors==
*2025.10: Theragen Bioinformatics Scientist of the Year Award by Korean Society for Bioinformatics (KSBI) 2025년 '''테라젠 올해의 생명정보인상''' (한국생명정보학회선정)
*2025.05: Yonsei University Golden Citations Award; 2025년 '''연세 최우수 피인용논문상''' (교신저자논문으로 1000회 이상 피인용 논문에 대한 수상) [https://www.yonsei.ac.kr/sc/183/subview.do#link 명예의 전당] 등재
*2025.04: Yonsei University Teaching Excellence Award; 2024년 연세 우수강의교수상
*2024.09: Yonsei University Underwood Distinguished Professor; '''연세 언더우드 특훈교수''' 선정
*2022.07: Yonsei University Faculty Research Award; 2021년 연세 우수업적교수상(연구부문, 논문업적분야)
*2022.05: Yonsei Academic Award (Field of Science and Engineering); 2022년 '''연세학술상'''(이학 공학 부문)
*2022.02: Yonsei University Teaching Excellence Award; 2021년 연세 우수강의교수상
*2019.02: Yonsei University Teaching Excellence Award; 2018년 연세 우수강의교수상
*2018.06: 28th The Outstanding Research Article Award in Science and Technology, The Korean Federation of Science and Technology Societies (KOFST); 제28회 과학기술우수논문상 (한국과학기술단체총연합회)
*2016.10: The Best Research Article of the Year 2017 in Animal Cells & Systems, The Korean Society for Integrative Biology; 한국통합생물학회 Animal Cells & Systems 최우수논문상
*2016.02: Yonsei University Teaching Excellence Award; 2015년 연세 우수강의교수상
*2015.01: Yonsei University Faculty Research Award; 2014년 연세 우수업적교수상(연구부문)
*2014.10: The Best Research Article of the Year 2014 in Animal Cells & Systems, The Korean Society for Integrative Biology; 한국통합생물학회 Animal Cells & Systems 최우수논문상
*2012.11: Top Ten Papers in Regulatory and Systems Genomics 2011, 5th Annual RECOMB Conference on Regulatory and Systems Genomics, San Francisco, Nov 12-15
*2012.09: Top 50 Basic Research Achievement Award by Korean National Research Foundation; 2012년 한국연구재단 우수성과 50선
*2011.12: ON-BIT Academic Award by Korean Society for Bioinformatics and Systems Biology (KSBSB) 2011년 '''온빛학술상''' (한국생명정보학회선정)
*2011.09: Top 50 Basic Research Achievement Award by Korean National Research Foundation 2011년 한국연구재단 우수성과 50선
*2011.02: Science magazine 2010 Visualization Challenge; A winner of Honorable Mention
*2010.11: POSCO TJ Park Junior Faculty Fellowship; 2010년 '''포스코 청암 사이언스펠로'''
*2010.02: Yonsei University Teaching Excellence Award; 2009년 연세 우수강의교수상

==Professional Experience==
*12/2024 – Present '''Chief Executive Officer (CEO)''', DECODE:BIOME Inc.
*09/2024 – Present '''Underwood Distinguished Professor''', Yonsei University ('''연세대 언더우드 특훈교수''')
*09/2024 – 06/2025 '''Advisory Committee Member''' The National Artificial Intelligence Commission ('''국가인공지능위원회 자문 위원 - AI 바이오 특별 위원회''')
*01/2023 – 12/2024 '''President''', Korean Society for Bioinformatics (KSBI) ('''한국생명정보학회 회장''')
*05/2022 – 02/2026 '''Affiliated Faculty''', POSTECH Biotech Center, Pohang University of Science and Technology (포스텍 겸임교수)
*01/2021 – 12/2022 '''Vice President''', Korean Society for Bioinformatics (KSBI) (한국생명정보학회 부회장)
*03/2020 – 02/2022 '''Department Chair''', Department of Biotechnology, Yonsei University
*09/2018 – 08/2020 '''Adjunct Professor''', Department of Biomedical Data Science & Systems Informatics, (의생명시스템정보학교실), Yonsei University College of Medicine
*03/2018 – 02/2019 '''Associate Dean''', College of Life Science and Biotechnology(생명시스템대학), Yonsei University
*03/2017 – Present '''Professor''', Department of Biotechnology, Yonsei University
*03/2016 – 02/2018 '''Program Chair''', Graduate Program in Biomaterials Science & Engineering (생물소재공학협동과정), Yonsei University
*03/2012 – 02/2017 '''Associate professor''', Department of Biotechnology, Yonsei University
*03/2008 – 02/2012 '''Assistant professor''', Department of Biotechnology, Yonsei University
*01/2006 – 02/2008 '''Research Associate''', Center for Systems and Synthetic Biology, University of Texas at Austin

==Editorial/Reviewer Board member==
*'''Genes''' (2019): Guest Editor (BIOINFO2019 special issue)
*'''Molecules and Cells''' (2018 – 2023): Editorial Board Member
*'''BMC Systems Biology''' (2017): Guest Editor (GIW2017 special issue)
*'''Scientific Reports (NPG)''' (2015 - 2020): Editorial Board Member (Genetics and Genomics category)
*'''Current Opinions in Plant Biology''' (2015): Guest Editor (Genome studies and molecular genetics)
*'''Animal Cells and Systems''' (2010 – 2020): Associate Editor
*'''Frontiers in Plant Science''' (2010 – 2018): Reviewer Board Member

==Invited Journal ''Ad hoc'' referee==
Nature Biotechnology, Nature Communications, Nature Protocols, Science Advances, Genome Research, Genome Biology, Genome Medicine, Nucleic Acids Research, Cancer Research, Bioinformatics, PLoS Genetics, PLoS Computational Biology, Scientific Reports, Trends in Plant Science, Plant Cell, Molecular Biology and Evolution, Plant Physiology, Journal of Plant Biology, BMC Systems Biology, BMC Bioinformatics, BMC Genomics, PROTEOMICS, PLoS One, Molecular Plant-Microbe Interactions, BioTechniques, IET-Systems Biology, and INFORMS Journal on Computing.

People:IS Lee

2026-01-29T14:55:17Z

Il1001: /* Awards and Honors */

__NOTOC__
{|
|[[File:insuklee_fixed.jpg|240px]]
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===Insuk Lee===
*[https://systemsbiology.yonsei.ac.kr/faculty/member.do?mode=view&userId=098A2bOKAr5Dnt%2B64UrHGg%3D%3D&sosokcd=1010495 Yonsei University Faculty Information]
*Department of Biotechnology
*50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
*Science Research Center S323 (Lab) S328 (Office)
*Office: +82-2-2123-5559
*Email: insuklee(at)yonsei(dot)ac(dot)kr

==Education==
*'''Postdoctoral training, Bioinformatics and Systems Biology''', University of Texas at Austin, TX (01/2003 – 12/2005)
*'''Ph.D., Microbiology''', University of Texas at Austin, TX (09/1996 – 12/2002)
*'''M.S., Biology''', Western Illinois University, Macomb, IL (09/1993 – 05/1996)
*'''B.S., Biology''', Hanyang University, Seoul, Korea (03/1986 – 02/1993, military service: 02/1988 – 05/1990)
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==Awards and Honors==
*2025.10: Theragen Bioinformatics Scientist of the Year Award by Korean Society for Bioinformatics (KSBI) 2025년 '''테라젠 올해의 생명정보인상''' (한국생명정보학회선정)
*2025.05: Yonsei University Golden Citations Award; 2025년 '''연세 최우수 피인용논문상''' (교신저자논문으로 1000회 이상 피인용 논문에 대한 수상) [https://www.yonsei.ac.kr/sc/183/subview.do#link 명예의 전당] 등재
*2025.04: Yonsei University Teaching Excellence Award; 2024년 연세 우수강의교수상
*2024.09: Yonsei University Underwood Distinguished Professor; '''연세 언더우드 특훈교수''' 선정
*2022.07: Yonsei University Faculty Research Award; 2021년 연세 우수업적교수상(연구부문, 논문업적분야)
*2022.05: Yonsei Academic Award (Field of Science and Engineering); 2022년 '''연세학술상'''(이학 공학 부문)
*2022.02: Yonsei University Teaching Excellence Award; 2021년 연세 우수강의교수상
*2019.02: Yonsei University Teaching Excellence Award; 2018년 연세 우수강의교수상
*2018.06: 28th The Outstanding Research Article Award in Science and Technology, The Korean Federation of Science and Technology Societies (KOFST); 제28회 과학기술우수논문상 (한국과학기술단체총연합회)
*2016.10: The Best Research Article of the Year 2017 in Animal Cells & Systems, The Korean Society for Integrative Biology; 한국통합생물학회 Animal Cells & Systems 최우수논문상
*2016.02: Yonsei University Teaching Excellence Award; 2015년 연세 우수강의교수상
*2015.01: Yonsei University Faculty Research Award; 2014년 연세 우수업적교수상(연구부문)
*2014.10: The Best Research Article of the Year 2014 in Animal Cells & Systems, The Korean Society for Integrative Biology; 한국통합생물학회 Animal Cells & Systems 최우수논문상
*2012.11: Top Ten Papers in Regulatory and Systems Genomics 2011, 5th Annual RECOMB Conference on Regulatory and Systems Genomics, San Francisco, Nov 12-15
*2012.09: Top 50 Basic Research Achievement Award by Korean National Research Foundation; 2012년 한국연구재단 우수성과 50선
*2011.12: ON-BIT Academic Award by Korean Society for Bioinformatics and Systems Biology (KSBSB) 2011년 '''온빛학술상''' (한국생명정보학회선정)
*2011.09: Top 50 Basic Research Achievement Award by Korean National Research Foundation 2011년 한국연구재단 우수성과 50선
*2011.02: Science magazine 2010 Visualization Challenge; A winner of Honorable Mention
*2010.11: POSCO TJ Park Junior Faculty Fellowship; 2010년 '''포스코 청암 사이언스펠로'''
*2010.02: Yonsei University Teaching Excellence Award; 2009년 연세 우수강의교수상

==Professional Experience==
*12/2024 – Present '''Chief Executive Officer (CEO)''', DECODE:BIOME Inc.
*09/2024 – Present '''Underwood Distinguished Professor''', Yonsei University ('''연세대 언더우드 특훈교수''')
*09/2024 – 06/2025 '''Advisory Committee Member''' The National Artificial Intelligence Commission ('''국가인공지능위원회 자문 위원 - AI 바이오 특별 위원회''')
*01/2023 – 12/2024 '''President''', Korean Society for Bioinformatics (KSBI) ('''한국생명정보학회 회장''')
*05/2022 – Present '''Affiliated Faculty''', POSTECH Biotech Center, Pohang University of Science and Technology (포스텍 겸임교수)
*01/2021 – 12/2022 '''Vice President''', Korean Society for Bioinformatics (KSBI) (한국생명정보학회 부회장)
*03/2020 – 02/2022 '''Department Chair''', Department of Biotechnology, Yonsei University
*09/2018 – 08/2020 '''Adjunct Professor''', Department of Biomedical Data Science & Systems Informatics, (의생명시스템정보학교실), Yonsei University College of Medicine
*03/2018 – 02/2019 '''Associate Dean''', College of Life Science and Biotechnology(생명시스템대학), Yonsei University
*03/2017 – Present '''Professor''', Department of Biotechnology, Yonsei University
*03/2016 – 02/2018 '''Program Chair''', Graduate Program in Biomaterials Science & Engineering (생물소재공학협동과정), Yonsei University
*03/2012 – 02/2017 '''Associate professor''', Department of Biotechnology, Yonsei University
*03/2008 – 02/2012 '''Assistant professor''', Department of Biotechnology, Yonsei University
*01/2006 – 02/2008 '''Research Associate''', Center for Systems and Synthetic Biology, University of Texas at Austin

==Editorial/Reviewer Board member==
*'''Genes''' (2019): Guest Editor (BIOINFO2019 special issue)
*'''Molecules and Cells''' (2018 – 2023): Editorial Board Member
*'''BMC Systems Biology''' (2017): Guest Editor (GIW2017 special issue)
*'''Scientific Reports (NPG)''' (2015 - 2020): Editorial Board Member (Genetics and Genomics category)
*'''Current Opinions in Plant Biology''' (2015): Guest Editor (Genome studies and molecular genetics)
*'''Animal Cells and Systems''' (2010 – 2020): Associate Editor
*'''Frontiers in Plant Science''' (2010 – 2018): Reviewer Board Member

==Invited Journal ''Ad hoc'' referee==
Nature Biotechnology, Nature Communications, Nature Protocols, Science Advances, Genome Research, Genome Biology, Genome Medicine, Nucleic Acids Research, Cancer Research, Bioinformatics, PLoS Genetics, PLoS Computational Biology, Scientific Reports, Trends in Plant Science, Plant Cell, Molecular Biology and Evolution, Plant Physiology, Journal of Plant Biology, BMC Systems Biology, BMC Bioinformatics, BMC Genomics, PROTEOMICS, PLoS One, Molecular Plant-Microbe Interactions, BioTechniques, IET-Systems Biology, and INFORMS Journal on Computing.

People:IS Lee

2026-01-29T14:54:40Z

Il1001: /* Awards and Honors */

__NOTOC__
{|
|[[File:insuklee_fixed.jpg|240px]]
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===Insuk Lee===
*[https://systemsbiology.yonsei.ac.kr/faculty/member.do?mode=view&userId=098A2bOKAr5Dnt%2B64UrHGg%3D%3D&sosokcd=1010495 Yonsei University Faculty Information]
*Department of Biotechnology
*50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
*Science Research Center S323 (Lab) S328 (Office)
*Office: +82-2-2123-5559
*Email: insuklee(at)yonsei(dot)ac(dot)kr

==Education==
*'''Postdoctoral training, Bioinformatics and Systems Biology''', University of Texas at Austin, TX (01/2003 – 12/2005)
*'''Ph.D., Microbiology''', University of Texas at Austin, TX (09/1996 – 12/2002)
*'''M.S., Biology''', Western Illinois University, Macomb, IL (09/1993 – 05/1996)
*'''B.S., Biology''', Hanyang University, Seoul, Korea (03/1986 – 02/1993, military service: 02/1988 – 05/1990)
|-
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|}

==Awards and Honors==
*2025.10: Theragen Bioinformatics Scientist of the Year Award Award by Korean Society for Bioinformatics (KSBI) 2025년 '''테라젠 올해의 생명정보인상''' (한국생명정보학회선정)
*2025.05: Yonsei University Golden Citations Award; 2025년 '''연세 최우수 피인용논문상''' (교신저자논문으로 1000회 이상 피인용 논문에 대한 수상) [https://www.yonsei.ac.kr/sc/183/subview.do#link 명예의 전당] 등재
*2025.04: Yonsei University Teaching Excellence Award; 2024년 연세 우수강의교수상
*2024.09: Yonsei University Underwood Distinguished Professor; '''연세 언더우드 특훈교수''' 선정
*2022.07: Yonsei University Faculty Research Award; 2021년 연세 우수업적교수상(연구부문, 논문업적분야)
*2022.05: Yonsei Academic Award (Field of Science and Engineering); 2022년 '''연세학술상'''(이학 공학 부문)
*2022.02: Yonsei University Teaching Excellence Award; 2021년 연세 우수강의교수상
*2019.02: Yonsei University Teaching Excellence Award; 2018년 연세 우수강의교수상
*2018.06: 28th The Outstanding Research Article Award in Science and Technology, The Korean Federation of Science and Technology Societies (KOFST); 제28회 과학기술우수논문상 (한국과학기술단체총연합회)
*2016.10: The Best Research Article of the Year 2017 in Animal Cells & Systems, The Korean Society for Integrative Biology; 한국통합생물학회 Animal Cells & Systems 최우수논문상
*2016.02: Yonsei University Teaching Excellence Award; 2015년 연세 우수강의교수상
*2015.01: Yonsei University Faculty Research Award; 2014년 연세 우수업적교수상(연구부문)
*2014.10: The Best Research Article of the Year 2014 in Animal Cells & Systems, The Korean Society for Integrative Biology; 한국통합생물학회 Animal Cells & Systems 최우수논문상
*2012.11: Top Ten Papers in Regulatory and Systems Genomics 2011, 5th Annual RECOMB Conference on Regulatory and Systems Genomics, San Francisco, Nov 12-15
*2012.09: Top 50 Basic Research Achievement Award by Korean National Research Foundation; 2012년 한국연구재단 우수성과 50선
*2011.12: ON-BIT Academic Award by Korean Society for Bioinformatics and Systems Biology (KSBSB) 2011년 '''온빛학술상''' (한국생명정보학회선정)
*2011.09: Top 50 Basic Research Achievement Award by Korean National Research Foundation 2011년 한국연구재단 우수성과 50선
*2011.02: Science magazine 2010 Visualization Challenge; A winner of Honorable Mention
*2010.11: POSCO TJ Park Junior Faculty Fellowship; 2010년 '''포스코 청암 사이언스펠로'''
*2010.02: Yonsei University Teaching Excellence Award; 2009년 연세 우수강의교수상

==Professional Experience==
*12/2024 – Present '''Chief Executive Officer (CEO)''', DECODE:BIOME Inc.
*09/2024 – Present '''Underwood Distinguished Professor''', Yonsei University ('''연세대 언더우드 특훈교수''')
*09/2024 – 06/2025 '''Advisory Committee Member''' The National Artificial Intelligence Commission ('''국가인공지능위원회 자문 위원 - AI 바이오 특별 위원회''')
*01/2023 – 12/2024 '''President''', Korean Society for Bioinformatics (KSBI) ('''한국생명정보학회 회장''')
*05/2022 – Present '''Affiliated Faculty''', POSTECH Biotech Center, Pohang University of Science and Technology (포스텍 겸임교수)
*01/2021 – 12/2022 '''Vice President''', Korean Society for Bioinformatics (KSBI) (한국생명정보학회 부회장)
*03/2020 – 02/2022 '''Department Chair''', Department of Biotechnology, Yonsei University
*09/2018 – 08/2020 '''Adjunct Professor''', Department of Biomedical Data Science & Systems Informatics, (의생명시스템정보학교실), Yonsei University College of Medicine
*03/2018 – 02/2019 '''Associate Dean''', College of Life Science and Biotechnology(생명시스템대학), Yonsei University
*03/2017 – Present '''Professor''', Department of Biotechnology, Yonsei University
*03/2016 – 02/2018 '''Program Chair''', Graduate Program in Biomaterials Science & Engineering (생물소재공학협동과정), Yonsei University
*03/2012 – 02/2017 '''Associate professor''', Department of Biotechnology, Yonsei University
*03/2008 – 02/2012 '''Assistant professor''', Department of Biotechnology, Yonsei University
*01/2006 – 02/2008 '''Research Associate''', Center for Systems and Synthetic Biology, University of Texas at Austin

==Editorial/Reviewer Board member==
*'''Genes''' (2019): Guest Editor (BIOINFO2019 special issue)
*'''Molecules and Cells''' (2018 – 2023): Editorial Board Member
*'''BMC Systems Biology''' (2017): Guest Editor (GIW2017 special issue)
*'''Scientific Reports (NPG)''' (2015 - 2020): Editorial Board Member (Genetics and Genomics category)
*'''Current Opinions in Plant Biology''' (2015): Guest Editor (Genome studies and molecular genetics)
*'''Animal Cells and Systems''' (2010 – 2020): Associate Editor
*'''Frontiers in Plant Science''' (2010 – 2018): Reviewer Board Member

==Invited Journal ''Ad hoc'' referee==
Nature Biotechnology, Nature Communications, Nature Protocols, Science Advances, Genome Research, Genome Biology, Genome Medicine, Nucleic Acids Research, Cancer Research, Bioinformatics, PLoS Genetics, PLoS Computational Biology, Scientific Reports, Trends in Plant Science, Plant Cell, Molecular Biology and Evolution, Plant Physiology, Journal of Plant Biology, BMC Systems Biology, BMC Bioinformatics, BMC Genomics, PROTEOMICS, PLoS One, Molecular Plant-Microbe Interactions, BioTechniques, IET-Systems Biology, and INFORMS Journal on Computing.

Publications

2026-01-25T06:26:49Z

Il1001: /* 2026 (6) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (6)==
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Review'''''
 
*131. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Revision'''''
 
*130. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Review'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*128. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2026-01-25T06:26:25Z

Il1001: /* 2026 (6) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (6)==
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Under Review'''''
 
*131. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Review'''''
 
*130. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Review'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*128. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

People

2026-01-14T10:04:59Z

Il1001: /* Scientists & Research Staff */

__NOTOC__
=='''Scientists & Research Staff'''==
{|border="0" width="1080"
|align="center"|[[File:prof_Insuk_fixed.png|100px|link=people:IS_Lee]]
|align="center"|[[File:SM_fixed.png|100px|link=people:SM_Yang]]
|align="center"|[[File:Ilseok_fixed.png|100px|link=People:IS_Choi]]
|align="center"|[[File:JunHyeong_fixed.png|100px|link=People:Jun_Hyung_Cha]]
|align="center"|[[File:JunYeong_fixed.png|100px|link=People:Junyeong_Ma]]
|align="center"|[[File:Hanjune_fixed.png|100px|link=People:Han-June_KIM]]
|align="center"|[[File:EuiJeong_fixed.png|100px|link=People:EuiJeong_Sung]]
|-

|width=160px; align="center"|[[people:IS_Lee|<big>'''Insuk Lee'''</big>]]
|width=160px; align="center"|[[people:SM_Yang|<big>'''Sunmo Yang'''</big>]]
|width=160px; align="center"|[[People:IS_Choi|<big>'''Ilseok Choi'''</big>]]
|width=160px; align="center"|[[People:Jun_Hyung_Cha|<big>'''Jun Hyung Cha'''</big>]]
|width=160px; align="center"|[[People:Junyeong_Ma|<big>'''Junyeong Ma'''</big>]]
|width=160px; align="center"|[[People:Hanjune_Kim|<big>'''Hanjune Kim'''</big>]]
|width=160px; align="center"|[[People:Euijeong_Sung|<big>'''Euijeong Sung'''</big>]]
|-

|align="center"|[[people:IS_Lee|Principal Investigator Professor]]
|align="center"|[[people:SM_Yang|Bioinformatics Programmer & Sys. Admin]]
|align="center"|[[People:IS_Choi|Ph.D candidate (Single-cell Biology) (2020.9 - )]]
|align="center"|[[People:Jun_Hyung_Cha|Ph.D candidate (Microbiome) (2020.9 - )]]
|align="center"|[[People:Junyeong_Ma|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Hanjune_Kim|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Euijeong_Sung|Ph.D candidate (Single-cell Biology) (2021.9 - )]]
|}
{|border="0" width="1080"

|align="center"|[[File:Sehun_fixed.png|100px|link=People:Sehun_Ahn]]
|align="center"|[[File:Jungyeon_fixed.png|100px|link=People:Jungyeon_Kim]]
|align="center"|[[File:Yerin_fixed.png|100px|link=People:Yerin_Kim]]
|align="center"|[[File:Yurim_fixed_(2).jpg|100px|link=People:Yurim_Jung]]
|align="center"|[[File:HaeBeen_fixed.jpg|100px|link=People:Hae_Been_lee]]
|align="center"|[[File:Sebin_fixed.jpg|100px|link=People:Sebin_Lim]]
|-
|width=160px; align="center"|[[People:Sehun_Ahn|<big>'''Sehun Ahn'''</big>]]
|width=160px; align="center"|[[People:Jungyeon_Kim|<big>'''Jungyeon Kim'''</big>]]
|width=160px; align="center"|[[People:Yerin_Kim|<big>'''Yerin Kim'''</big>]]
|width=160px; align="center"|[[People:Yurim_Jung|<big>'''Yurim Jung'''</big>]]
|width=160px; align="center"|[[People:Hae_Been_lee|<big>'''Hae Been Lee'''</big>]]
|width=160px; align="center"|[[People:Sebin_Lim|<big>'''Sebin Lim'''</big>]]
|-
|align="center"|[[People:Sehun_Ahn|Ph.D candidate (Microbiome) (2022.3 - )]]
|align="center"|[[People:Jungyeon_Kim|Integrated Ph.D candidate (Microbiome) (2023.3 - )]]
|align="center"|[[People:Yerin_Kim|Integrated Ph.D course (Microbiome) (2024.3 - )]]
|align="center"|[[People:Yurim_Jung|Integrated Ph.D course (Single-cell Biology) (2024.9 - )]]
|align="center"|[[People:Hae_Been_lee|Integrated Ph.D course (Microbiome) (2024.9 - )]]
|align="center"|[[People:Sebin_Lim|Integrated Ph.D course (Microbiome) (2025.3 - )]]
|}

=='''Administrative Assistant'''==

=='''Undergraduate Students'''==
*Zunu An
*Seung Wan Jeon
*Yunyeong Jang
*Jong Hyun Hwang
*Sung Min Kim
*Zixuan Guo
*Hyeonjin Kim
*Eunjeong Kim

=='''Alumni'''==
*'''Former Post-docs and Staff Scientists'''
**1. Taeyun Oh (2009.5-2011.12), currently Senior Researcher at Cowellbiogim, Korea
**2. Sohyun Hwang (2010.3-2015.8), currently Professor at [https://grad.cha.ac.kr/%ed%99%a9%ec%86%8c%ed%98%84/ Department of Biomedical Science, CHA University], Korea [https://scholar.google.com/citations?user=z5yC9cwAAAAJ&hl=en Google Scholar] (차의과대학 의과학과 교수)
**3. Samuel Beck (2011.2-2011.12), currently Associate Professor at Boston University, USA, [https://beck310.wixsite.com/becklab Lab Homepage] (미 보스턴 대학교 부교수)
**4. Jawon Song (2011.1-2012.5), currently Research Associate at [https://www.tacc.utexas.edu/about/directory/jawon-song Texas Advanced Computing Center], Austin, TX, USA [https://scholar.google.com/citations?user=wv61wGoAAAAJ&hl=en Google Scholar] (미국 텍사스슈퍼컴퓨팅센터 선임연구원)
**5. Yoonhee Ko (2012.8-2014.2), currently Associate Professor at [https://hufsbiomed.weebly.com/ Department of Biomedical Engineering, Hankuk University of Foreign Studies], Korea [https://scholar.google.com/citations?user=GBxCYX8AAAAJ&hl=en Google Scholar] (한국외국어대 바이오공학과 교수)
**6. Jonghoon Lee (2013.10-2014.2), currently Professor at [https://www.gachon.ac.kr/foodbiotech/6142/subview.do Department of Food Biotechnology, Gachon University], Korea (가천대학교 식품생명공학과 교수)
**7. Jung Eun Shim (2009.8-2017.11), currently Staff Scientist at Yonsei Genomics Center Bioinformatics Data Analysis Core (연세의료원 유전체센터 생명정보분석코어 책임연구원)

*'''Former Graduate Students (Ph.D)'''
**1. Junha Shin (2008.9-2014.2), PhD; currently Scientist at [https://wid.wisc.edu/people/junha-shin/ Wisconsin Institute for Discovery], USA (미국 위스콘신 대학연구소 연구원)
**2. Hanhae Kim (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**3. Ara Cho (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**4. Eiru Kim (2010.9-2016.8), PhD; currently Senior Expert in Data Science, [https://www.gnf.org/ The Genomics Institute of the Novartis Research Foundation], San Diego, USA (노바티스 선임데이터분석연구원)
**5. Tak Lee (2011.3-2017.2), PhD; currently Senior Bioinformatician, [https://www.mpipz.mpg.de/en Max Planck Institute for Plant Breeding Research] (독일 막스플랭크 연구소 선임생명정보학자)
**6. Heonjong Han (2013.3~2019.8), PhD; currently Bioinformatics engineer at [https://3billion.io/ 3billion] (바이오기업 데이터사이언티스트)
**7. Kyungsoo Kim (2013.3~2020.2), PhD; currently Research Professor at Severance Hospital (강남세브란스의료원 유방암센터 연구교수)
**8. Jae-Won Cho (2016.9~2021.2), PhD; currently Assistant Professor at [https://ibb.hanyang.ac.kr/ Hanyang Institute of Bioscience and Biotechnology] (한양대학교 한양생명과학기술원 조교수)
**9. Chan Yeong Kim (2015.3~2021.2), PhD; currently Postdoc Fellow at European Molecular Biology Laboratory in Heidelberg [http://www.bork.embl.de/j/ Bork Group] (유럽연합분자생물학연구소 박사후 연구원)
**10. Sungho Lee (2017.3-2024.2), PhD; currently Data Scientist at [http://www.mogam.re.kr/kor/ MOGAM Institute for Biomedical Research] (목암생명과학연구소, (주)녹십자 출연 연구소, 선임연구원)
**11. Junha Cha (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://dna-discovery.stanford.edu/ Prof. Hanlee P. Ji Lab](미국 스탠퍼드대학교 박사후연구원)
**12. Seungbyn Baek (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://kundajelab.github.io/ Prof. Anshul Kundaje Lab](미국 스탠퍼드대학교 박사후연구원)
**13. Nayeon Kim (2019.9-2025.2), PhD; currently Postdoc Fellow at KAIST InnoCORE Research Group (과학기술원 InnoCORE 초거대언어모델 혁신 연구단, 박사후연구원)

*'''Former Graduate Students (Master's degree)'''
**1. Sun-Gou Ji (2009.9-2011.8), M.Eng.; PhD from University of Cambridge (Sanger Genome center); currently Vice President, Computational Genetics at [https://bridgebio.com/ BridgeBio Pharma], Boston, USA (미 바이오기업 부대표)
**2. Hyojin Kim (2013.3-2015.2), M.Eng.; PhD from University of Aachen; currently Scientist at Bayer, Germany [https://www.linkedin.com/in/hyojin-kim-b3bb711ab Linkedin] (독일 바이엘 제약회사 선임 연구원)
**3. Hongseok Shim (2013.9-2015.8), M.Eng.; currently PhD student, Arizona State University, Biomedical Informatics program (애리조나주립대 생물정보학 박사과정)
**4. Sunmo Yang (2014.9-2017.2), M.Eng. currently Bioinformatics programmer, Yonsei University (연세대 네트워크생명공학 연구실 책임데이터연구원)
**5. Muyoung Lee (2016.3-2018.2), M.Eng. currently PhD student, University of Texas at Austin, Cellular and Molecular Biology Program (텍사스주립대 생물정보학 박사과정)
**6. Jiwon Yu (2021.9-2023.8), M.Eng. currently Data Scientist at [https://www.samsungbioepis.com/kr/index.do SAMSUNG BIOEPIS] (삼성바이오에피스 데이터사이언티스트)
**7. Geon_Koh (2022.9-2025.2), M.Eng. currently Researcher at Gachon University, College of Medicine (가천의대 시스템생물학 연구실 연구원)
**8. Wonjong Kim (2023.3-2025.8), M.Eng. currently Researcher at [https://samsungbiologics.com/ SAMSUNG Biologics] (삼성바이오로직스 연구원)

*'''Former Visiting Scientists/Students'''
**1. Minkyung Shin (2012.3-2012.7), went to University of Southern California graduate school
**2. Paul Chung (2012 summer), currently work at [https://about.meta.com/ Meta], USA
**3. Hyunjin Cho (2014 summer), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA
**4. Michael Chung (2016.8-2016.12), currently work at [https://about.meta.com/ Meta], USA

*'''Former Undergraduate Students'''
**1. Ila Shin, went to medical school (Yonsei Univ.) Currently Professor, Kyunghee University School of Medicine (경희대학교 의과대학 교수)
**2. Yoonkyung Ko
**3. Sangyo Park, went to law school (Kyounghee Univ.)
**4. Jayoon Shin, went to medical school (Pusan National Univ.)
**5. Dongjoo Sun, went to dental school (Wongwang Univ.)
**6. Eulsoo Kim
**7. Myungwhan Lee, went to medical school (Yonsei Univ.)
**8. Moonhee Lee, went to graduate school (University of Amsterdam, Netherlands)
**9. Jinhyun Ju, went to graduate school (Cornell Medical School, Computational Systems Biology); Currently Principal Computational Biologist, Cancer Genomics at [https://bridgebio.com/ BridgeBio Pharma], Seattle, USA (미 바이오기업 선임연구원)
**10. Haeyoung Shin, went to graduate school (Brown University, Computational Neuroscience); Currently Professor, Seoul National University (서울대학교 생명과학부 교수)
**11. Joonghee Soh, went to graduate school (KAIST, Culture Technology)
**12. Hee Jung Cho, went to graduate school (UC Berkeley)
**13. TaeHwan Kim, went to medical school
**14. Joohyung Kim, went to medical school (Kyungpook National Univ.)
**15. Donghyun Shin, went to medical school (Yonsei Univ.)
**16. Byunghee Kang (2015 spring - 2016 summer), went to graduate school (PosTech)
**17. Sunphil Kim (2016 winter)
**18. Jaeho Shim (2016 winter)
**19. Seunghyun Shin (2016 spring)
**20. Aejoo Hong (2016 spring)
**21. Changbae Bang (2016 summer), went to medical school (Yonsei Univ.)
**22. Seoyoung Choi (2016 summer)
**23. Dabin Jung (2016 summer)
**24. Boreum Nam (2016 summer)
**25. Seungun Lee (2016 summer)
**26. Yeaji Kim (2016 summer and fall)
**27. Sangyoung Lee (2017 winter)
**28. Heejun Jang (2017 winter & spring), went to KIST as Research Assistant
**29. Jungha Lee (2017 summer), went to graduate school (Seoul National Univ.)
**30. Seunghyun Wang (2017 summer), went to graduate school (KAIST)
**31. Dong-Min Yang (2017 fall)
**32. Doo-Hee Lee (2017 fall)
**33. Suk-Jae Han (2018 winter)
**34. Ji-Eun Han (2018 winter)
**35. Yuri Ko (2018 spring)
**36. Sung-Woo Kim (2018 spring)
**37. Woosung Kwon (2018 summer)
**38. Soyun Kong (2018 summer)
**39. Hojeong Keum (2018 summer and fall)
**40. Sungjun Lim (2018 summer and fall)
**41. Jiyoon Lee (2018 summer and fall)
**42. Ilseok Choi(2019 winter, spring, summer and fall, 2020 winter, spring)
**43. Junik Park (2019 winter)
**44. Lee Yoo (2019 winter & spring)
**45. Yeonwha Kim (2019 winter & spring)
**46. Sohee Kim (2019 spring)
**47. Juseong Lee (2019 spring)
**48. Junyoung Yang (2019 spring & summer)
**49. Junyeong Ma (2019 summer, 2020 winter, summer, fall, 2021 winter)
**50. Dayeon Jung (2019 summer)
**51. Hanjoon Kim (2019 summer, 2021 winter)
**52. Hyungjin Kim (2020 winter, spring)
**53. Sujin Hyun (2020 winter)
**54. Hyuki Lee (2020 winter)
**55. Donghwan Lee (2020 winter)
**56. Jun Hyung Cha (2020 spring, summer)
**57. Jiwon Yu (2020 summer, 2021 Spring, summer)
**58. Dong Seok Kim (2020 summer)
**59. Donggeun Lee (2020 summer)
**60. Sehun Ahn (2020 summer, 2021 winter, spring, summer, 2022 winter)
**61. Jiho Kim (2020 summer)
**62. Euijung Seong (2020 fall, 2021 spring, summer)
**63. Junhan Kim (2021 winter & spring)
**64. Suyong Choi (2021 winter)
**65. Sujin Pyeon (2021 Spring)
**66. Hyeon Hee Ji (2021 Spring)
**67. Semin Kim (2021 Summer)
**68. Su Hwan Kim (2021 Summer)
**69. Yongbin Kim (2021 Summer)
**70. Nan Park (2021 Summer)
**71. Hoyong Jung (2021 Summer)
**72. Ingyeong Koh (2021 Summer)
**73. Jongbin Jeong (2022 Winter)
**74. Sungchul Yang (2022 Winter, Spring, Summer)
**75. Hyojung Lee (2022 Winter, Spring)
**76. Jun Hyeong Kim (2022 Winter, Spring)
**77. Young Ji Roh (2022 Spring, Summer)
**78. Geon Koh (2022 Spring, Summer)
**79. Hayoung Kang (2022 Summer, 2023 Spring)
**80. Won Jong Kim (2022 Summer, Fall, 2023 Winter)
**81. Christian Lee (2022 Summer)
**82. Je Yun Kang (2022 Summer)
**83. Sumin Lee (2022 Fall)
**84. Jungyeon Kim (2022 Fall, 2023 Winter)
**85. Seol Song (2023 Winter)
**86. Soyeon Kim (2023 Summer)
**87. Sieun Park (2023 Summer)
**88. Gunhyeong Lee (2023 Summer)
**89. Yunseo Han (2023 Summer)
**90. Jae Hyun Kim (2023 Summer)
**91. Jeong-min Seo (2023 Summer)
**92. Yerin Kim (2023 Fall, 2024 Winter)
**93. Sang Min Park (2024 Winter)
**94. Minsun Seo (2024 Winter)
**95. Jaeryun Sim (2024 Winter)
**96. Sun Min Lim (2024 Winter)
**97. Yurim Jung (2024 Spring, Summer)
**98. Hae Been Lee (2024 Spring, Summer)
**99. Zunu An (2024 Summer, Fall, 2025 Winter, Spring, Summer)
**100. Se Bin Lim (2024 Summer, Fall, 2025 Winter)
**101. Sang Min Yoon (2024 Summer)
**102. Yena Kim (2024 Summer)
**103. Kang Eon Lee (2024 Fall)
**104. Soyoon Park (2025 Winter)
**105. Sojung Lee (2025 Winter)
**106. Leanne Ma (2025 Winter)
**107. Seung Wan Jeon (2025 Summer)
**108. Joongun Lee (2025 Summer)
**109. Minseo Kim (2025 Summer)
**110. Hong Kyu Park (2025 Summer)
**111. Yunyeong Jang (2025 Fall, 2026 Winter)
**112. Jong Hyun Hwang (2025 Fall, 2026 Winter)
**113. Gyuweon Park (2025 Fall)

Publications

2026-01-08T00:23:01Z

Il1001:

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (6)==
*132. Incorporating viral genome binning in a mouse gut virome catalog enables accurate age prediction '''''Submitted'''''
 
*131. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Review'''''
 
*130. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Review'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*128. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2026 Jan 6; 11(1):317-334 [https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 

==2025 (10)==
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Media & Outreach

2025-12-09T00:15:20Z

Il1001:

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*2025 Dec 08
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*2025 July 24
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*2025 July 14
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*2024 Dec 31
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동아일보
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[https://www.donga.com/news/Health/article/all/20241230/130756741/2 “면역항암제 효과 높이는 핵심 단백질 발견"]
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*2024 Dec 16
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연세소식
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[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20241216171238142043&sr_site=S&sr_volume=636 언더우드 특훈교수 선정, 고원건‧김근수‧김현우‧박태영‧서지원‧염유식‧이인석 교수 세계적 수준의 연구 성과로 인류 발전에 기여]
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*2024 Sept 11
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*2024 June 27
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연세소식
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[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20240619104047616012&sr_volume=636 [연구 프론티어] 생명시스템대학·의료원 공동연구팀, 인유두종바이러스 양성 두경부암의 정밀 면역항암치료 타겟 제시]
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중앙일보
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SBS News
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*2024 Feb 16
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연합뉴스
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[https://www.yna.co.kr/view/AKR20240216069000004 미세플라스틱 섭취, 장 누수 유발·염증성 장질환 악화]
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*2022 Dec 29
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조선일보
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연세소식
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교수신문
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연세소식
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*2022 Nov 1
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디지털타임스
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*2022 April 20
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연세소식
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*2021 Oct 19
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헬스조선
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[https://health.chosun.com/site/data/html_dir/2021/10/19/2021101901179.html 폐암 환자, 면역항암제 반응 예측 가능해져… 맞춤형 치료 가능성↑]
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*2021 Oct 19
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연세소식
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[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20211019095335963012&sr_volume=630&list_mode=list&sr_site=S&pager.offset=0&sr_cates=25 생명시스템대학·의과대학 연구팀, 단일세포 유전체 분석 기반 비소세포폐암 치료반응 예측 시그니처 발굴]
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*2021 Sep 7
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연세소식영문판
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*2020 Mar 16
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{|border="0"
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*2018 Dec 04
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연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20181204123907677066&sr_volume=619&list_mode=list&sr_site=S&pager.offset=0&sr_cates=25 이인석 교수 연구팀, 시스템의학을 위한 휴먼유전자네트워크 개발]
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{|border="0"
| width="100"|
*2017 Dec 05
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연세소식
|
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|}
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{|border="0"
| width="100"|
*2017 June 01
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연세소식
|
[[media:GWAB_yonsei.pdf|이인석 교수 연구팀, 유전체코호트 네트워크 분석을 통한 질병 유전자 예측 시스템 개발]]
|}
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{|border="0"
| width="100"|
*2016 Dec 06
|width="200" align="center"|
연세소식
|
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|}
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{|border="0"
| width="100"|
*2016 Nov 14
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연세춘추
|
[[media:20161114-연세춘추-이인석.pdf|암유전자의 소셜네트워크를 보다]]
|}
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{|border="0"
| width="100"|
*2016 Sep 2
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연세소식
|
[[media:201609-연세소식-이인석.pdf|이인석 교수팀, 유전자 소셜 네트워크로 암유전자 찾아낸다]]
|}
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| width="100"|
*2016 June 27
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연합뉴스
|
[http://www.yonhapnews.co.kr/bulletin/2016/06/25/0200000000AKR20160625014300017.HTML?input=1195m 네트워크' 이용해 암 유전자 찾는 새 시스템 개발]
|}
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{|border="0"
| width="100"|
*2016 June 27
|width="200" align="center"|
매일경제
|
[http://news.mk.co.kr/newsRead.php?no=457258&year=2016 유전자 소셜 네트워크로 癌유발 유전자 찾는다]
|}
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{|border="0"
| width="100"|
*2016 June 27
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동아일보
|
[http://news.donga.com/3/all/20160626/78865398/1 국내 연구진, 희귀암 등 새로운 암 유발 유전자 찾는 시스템 개발]
|}
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{|border="0"
| width="100"|
*2016 June 27
|width="200" align="center"|
YTN Science
|
[http://science.ytn.co.kr/program/program_view.php?s_mcd=0082&s_hcd=&key=201606271111574798 유전자 지도로 암 유발 유전자 예측]
|}
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{|border="0"
| width="100"|
*2016 Feb 4
|width="200" align="center"|
연세소식
|
[[media:역분화인자발굴.pdf|이인석 교수 연구팀, 시스템생물학 기반 줄기세포 역분화 효율 증진인자 발굴]]
|}
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{|border="0"
| width="100"|
*2015 Dec 7
|width="200" align="center"|
연세소식
|
[[media:연세소식기사_MouseNet.pdf|이인석 교수 연구팀, 세계 최대 규모 실험용 흰쥐 유전자 네트워크 MouseNet 개발]]
|}
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{|border="0"
| width="100"|
*2015 April 16
|width="200" align="center"|
연세소식
|
[[media:Yonseisosik.pdf|이인석 교수 연구팀, 빅데이터 기반 유전자네트워크를 이용한 작물연구 관련 종설과 연구논문 발표]]
|}
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{|border="0"
| width="100"|
*2014 Oct 30
|width="200" align="center"|
Yonsei Research Magazine
|
[[media:Yonsei_Research_Magazine.pdf|Professor Lee Insuk's Research Team Finds a New Way to Study Human Diseases]]
|}
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{|border="0"
| width="100"|
*2014 July 16
|width="200" align="center"|
ScienceTimes
|
[http://www.sciencetimes.co.kr/?news=%EC%A7%88%EB%B3%91-%EC%B9%98%EB%A3%8C-%EC%A0%95%ED%99%95%ED%95%9C-%EC%9B%90%EC%9D%B8%EC%A7%84%EB%8B%A8%EC%9D%B4-%EB%A8%BC%EC%A0%80%EC%A3%A0 “질병 치료, 정확한 원인진단이 먼저죠”]
|}
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{|border="0"
| width="100"|
*2014 June 25
|width="200" align="center"|
한국경제
|
[[media:morphin_article.jpg|유전자-질환 연관성 예측시스템 나왔다]]
|}
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{|border="0"
| width="100"|
*2014 June 24
|width="200" align="center"|
YTN Science
|
[https://www.youtube.com/watch?v=tpiGS5cArY4 유전자 상관관계 네트워크로 질환 연구]
|}
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{|border="0"
| width="100"|
*2012 Nov 22
|width="200" align="center"|
5th RECOMB Conference on Regulatory and Systems Genomics
|
[http://recomb-2012.c2b2.columbia.edu/?q=node/29 HumanNet 논문(Genome Research 21:1109)이 2011년 시스템생물학 분야에서 가장 영향력 있는 논문 탑10에 선정]
|}
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{|border="0"
| width="100"|
*2011 Nov 9
|width="200" align="center"|
YTN Science 24
|
[http://www.sciencetv.kr/program/program_view.php?s_mcd=0184&s_hcd=01&key=201111091542149116 벼 유전자 네트워크 완성...슈퍼 벼 생산]
|}
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{|border="0"
| width="100"|
*2011 Nov 1
|width="200" align="center"|
KBS News
|
[http://news.kbs.co.kr/science/2011/11/01/2381579.html 병충해·홍수에 강한 ‘슈퍼 벼’ 개발]

보도내용 중 이화여대연구진을 연세대학교 연구진 으로 정정합니다
|}
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{|border="0"
| width="100"|
*2011 Nov 1
|width="200" align="center"|
Dong-A Ilbo Channel A News
|
[http://news.donga.com/3/all/20111104/41645483/1 벼 유전자 네트워크]
|}
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{|border="0"
| width="100"|
*2011 Oct 3
|width="200" align="center"|
The financial news
|
[[media:Media_n_Outreach_019.pdf|한국 과학의 미래，이젠 노벨상이다(2): ④ 미로처럼 얽힌 유전자 네트워크 지도화]]

|}
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{|border="0"
| width="100"|
*2011 Aug 31
|width="200" align="center"|
MBN News
|
[http://tvnews.media.daum.net/view.html?cateid=100000&newsid=20110831141310630&p=mbn[수요일에 만난 과학자] 유전자의 소셜 네트워크를 밝힌다
]

|}
----

{|border="0"
| width="100"|
*2011 May
|width="200" align="center"|
KBS News
|
[http://news.kbs.co.kr/science/2011/05/12/2290284.html '휴먼 넷' 난치성 질환 치료 해법 찾아]

|}
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{|border="0"
| width="100"|
*2011 May
|width="200" align="center"|
News Letter Yonsei
|
[[media:Media_n_Outreach_018.pdf|유전자 소셜 네트워크로 암, 당뇨 조절 유전자 발굴법 개발]]

|}
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{|border="0"
| rowspan = "2" width="100"|
*2011 May
|width="200" align="center"|
Digital times
|
[[media:Media_n_Outreach_017.pdf|유전자 네트워크로 질병 규명]]
|-
|width="200" align="center"|
The Kyunghyang Daily News
|
[[media:Media_n_Outreach_017.pdf|유전자와 유전자의 '관계' 네트워크 지도 개발]]
|}
----
{|border="0"
| width="100"|
*2011 Feb
|width="200" align="center"|
The Chosunilbo
|
[[media:Media_n_Outreach_016.pdf|인간 세상 네트워크 닮은 식물 유전자의 세계]]

|}
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{|border="0"
| width="100"|
*2011 Feb
|width="200" align="center"|
Science : Visualization Challenge
|
[[media:Media_n_Outreach_015.pdf|AraNet: A Genome-wide Gene Function Association Network for ''Arabidopsis thaliana'']]

|}
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{|border="0"
| width="100"|
*2010 Nov
|width="200" align="center"|
POSCO News
|
[[media:Media_n_Outreach_014.pdf|'2011청암펠로우(이인석 교수 선정)]]

|}
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{|border="0"
| width="100"|
*2010 Sep
|width="200" align="center"|
News Letter Yonsei
|
[[media:Media_n_Outreach_013.pdf|생명공학과 학부생 연구결과 국제 권위 저널에 실려 (김이루 학생)]]

|}
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{|border="0"
| width="100"|
*2010 Aug
|width="200" align="center"|
The Chosunilbo
|
[[media:Media_n_Outreach_012.pdf|연세대 학부생 생명공학 논문 국제학술지 게재 (김이루 학생)]]

|}
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{|border="0"
| width="100"|
*2010 Aug
|width="200" align="center"|
The Science & technology
|
[[media:Media_n_Outreach_011.pdf|유전자네트워크 이용한 복잡질환 조절유전자 예측방법 개발 (논단)]]

|}
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{|border="0"
| width="100"|
*2010 Jul
|width="200" align="center"|
News Letter Yonsei
|
[[media:Media_n_Outreach_010.pdf|이인석 교수, 암,당뇨 등의 새로운 치료법 가능성 열어]]

|}
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{|border="0"
| rowspan = "2" width="100"|
*2010 Jun
|width="200" align="center"|
Kukminilbo
|
[[media:Media_n_Outreach_009.pdf|암,당뇨병 등 복잡 질환 조절 유전자 효율적으로 찾아내는 새로운 방법 개발]]
|-
|width="200" align="center"|
Seoul newspaper
|
[[media:Media_n_Outreach_009.pdf|암,당뇨 등 '조절 유전자 예측법' 개발]]
|}
----
{|border="0"
| width="100"|
*2010 Mar
|width="200" align="center"|
The Yonsei Chunchu (Daily newspaper of Yonsei University)
|
[[media:Media_n_Outreach_008.pdf|'예측'이 가장 쉬웠어요]]

|}
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{|border="0"
| width="100"|
*2010 Mar
|width="200" align="center"|
News Letter Yonsei
|
[[media:Media_n_Outreach_007.pdf|이인석교수, 세계 최대 식물유전자네트워크 규명]]

|}
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{|border="0"
| width="100"|
*2010 Mar
|width="200" align="center"|
The Science & technology
|
[[media:Media_n_Outreach_006.pdf|네트워크 이용한 새롭고 효율적인 유전학 연구 기법 제시 (논단)]]

|}
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{|border="0"
| width="100"|
*2010 Mar
|width="200" align="center"|
Biomedical Computation Review (IT magazine)
|
[[media:Media_n_Outreach_005.pdf|A Tipping Point for Function Prediction]]

|}
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{|border="0"
| width="100"|
*2010 Feb
|width="200" align="center"|
The Korea Economic Daily
|
[[media:Media_n_Outreach_004.pdf|식물도 사람처럼 유전자 네트워크가 있었네!]]

|}
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{|border="0" width="730"
| width="100"|
*2010 Feb
|width="200" align="center"|
The Chosunilbo
|
[[media:Media_n_Outreach_003.pdf|유전자 숨겨진 기능 쉽게 찾는 '네트워크 기술']]

|}
----
{|border="0"
| width="100"|
*2010 Feb
|width="200" align="center"|
Science Daily
|
[[media:Media_n_Outreach_002.pdf|Gene Function Discovery: New Computation Model Predicts Gene Function]]

|}
----
{|border="0"
|width="100"|
*2008 Dec
|width="200" align="center"|
KSMCB (Korean Society for Molecular and Cellular Biology) news
|
[[media:Media_n_Outreach_001.pdf|기능성유전자 네트워크를 이용한 생물학 연구 (논단)]]

|}
----

Publications

2025-12-05T11:26:42Z

Il1001: /* 2025 (11) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (4)==
*131. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Review'''''
 
*130. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Review'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*128. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 

==2025 (11)==
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' 2025 Dec 4. Online ahead of print.[https://pubmed.ncbi.nlm.nih.gov/41345261/ pubmed][https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2025-12-04T11:28:36Z

Il1001: /* 2026 (2) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (4)==
*131. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Review'''''
 
*130. DNA-barcoded extracellular vesicles enable the identification and characterization of recipient cells in the lung, '''''Under Review'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*128. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 

==2025 (11)==
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' Accepted [https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2025-12-04T11:21:23Z

Il1001:

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (2)==
*130. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Review'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
*128. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 
==2025 (11)==
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' Accepted [https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

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2025-12-04T08:38:21Z

Il1001: /* Alumni */

__NOTOC__
=='''Scientists & Research Staff'''==
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|align="center"|[[File:JunHyeong_fixed.png|100px|link=People:Jun_Hyung_Cha]]
|align="center"|[[File:JunYeong_fixed.png|100px|link=People:Junyeong_Ma]]
|align="center"|[[File:Hanjune_fixed.png|100px|link=People:Han-June_KIM]]
|align="center"|[[File:EuiJeong_fixed.png|100px|link=People:EuiJeong_Sung]]
|-

|width=160px; align="center"|[[people:IS_Lee|<big>'''Insuk Lee'''</big>]]
|width=160px; align="center"|[[people:SM_Yang|<big>'''Sunmo Yang'''</big>]]
|width=160px; align="center"|[[People:IS_Choi|<big>'''Ilseok Choi'''</big>]]
|width=160px; align="center"|[[People:Jun_Hyung_Cha|<big>'''Jun Hyung Cha'''</big>]]
|width=160px; align="center"|[[People:Junyeong_Ma|<big>'''Junyeong Ma'''</big>]]
|width=160px; align="center"|[[People:Hanjune_Kim|<big>'''Hanjune Kim'''</big>]]
|width=160px; align="center"|[[People:Euijeong_Sung|<big>'''Euijeong Sung'''</big>]]
|-

|align="center"|[[people:IS_Lee|Principal Investigator Professor]]
|align="center"|[[people:SM_Yang|Bioinformatics Programmer & Sys. Admin]]
|align="center"|[[People:IS_Choi|Ph.D candidate (Single-cell Biology) (2020.9 - )]]
|align="center"|[[People:Jun_Hyung_Cha|Ph.D candidate (Microbiome) (2020.9 - )]]
|align="center"|[[People:Junyeong_Ma|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Hanjune_Kim|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Euijeong_Sung|Ph.D candidate (Single-cell Biology) (2021.9 - )]]
|}
{|border="0" width="1080"

|align="center"|[[File:Sehun_fixed.png|100px|link=People:Sehun_Ahn]]
|align="center"|[[File:Jungyeon_fixed.png|100px|link=People:Jungyeon_Kim]]
|align="center"|[[File:Yerin_fixed.png|100px|link=People:Yerin_Kim]]
|align="center"|[[File:Yurim_fixed_(2).jpg|100px|link=People:Yurim_Jung]]
|align="center"|[[File:HaeBeen_fixed.jpg|100px|link=People:Hae_Been_lee]]
|align="center"|[[File:Sebin_fixed.jpg|100px|link=People:Sebin_Lim]]
|-
|width=160px; align="center"|[[People:Sehun_Ahn|<big>'''Sehun Ahn'''</big>]]
|width=160px; align="center"|[[People:Jungyeon_Kim|<big>'''Jungyeon Kim'''</big>]]
|width=160px; align="center"|[[People:Yerin_Kim|<big>'''Yerin Kim'''</big>]]
|width=160px; align="center"|[[People:Yurim_Jung|<big>'''Yurim Jung'''</big>]]
|width=160px; align="center"|[[People:Hae_Been_lee|<big>'''Hae Been Lee'''</big>]]
|width=160px; align="center"|[[People:Sebin_Lim|<big>'''Sebin Lim'''</big>]]
|-
|align="center"|[[People:Sehun_Ahn|Ph.D candidate (Microbiome) (2022.3 - )]]
|align="center"|[[People:Jungyeon_Kim|Integrated Ph.D course (Microbiome) (2023.3 - )]]
|align="center"|[[People:Yerin_Kim|Integrated Ph.D course (Microbiome) (2024.3 - )]]
|align="center"|[[People:Yurim_Jung|Integrated Ph.D course (Single-cell Biology) (2024.9 - )]]
|align="center"|[[People:Hae_Been_lee|Integrated Ph.D course (Microbiome) (2024.9 - )]]
|align="center"|[[People:Sebin_Lim|Integrated Ph.D course (Microbiome) (2025.3 - )]]
|}

=='''Administrative Assistant'''==

=='''Undergraduate Students'''==
*Zunu An
*Seung Wan Jeon
*Yunyeong Jang
*Jong Hyun Hwang
*Sung Min Kim
*Zixuan Guo
*Hyeonjin Kim
*Eunjeong Kim

=='''Alumni'''==
*'''Former Post-docs and Staff Scientists'''
**1. Taeyun Oh (2009.5-2011.12), currently Senior Researcher at Cowellbiogim, Korea
**2. Sohyun Hwang (2010.3-2015.8), currently Professor at [https://grad.cha.ac.kr/%ed%99%a9%ec%86%8c%ed%98%84/ Department of Biomedical Science, CHA University], Korea [https://scholar.google.com/citations?user=z5yC9cwAAAAJ&hl=en Google Scholar] (차의과대학 의과학과 교수)
**3. Samuel Beck (2011.2-2011.12), currently Associate Professor at Boston University, USA, [https://beck310.wixsite.com/becklab Lab Homepage] (미 보스턴 대학교 부교수)
**4. Jawon Song (2011.1-2012.5), currently Research Associate at [https://www.tacc.utexas.edu/about/directory/jawon-song Texas Advanced Computing Center], Austin, TX, USA [https://scholar.google.com/citations?user=wv61wGoAAAAJ&hl=en Google Scholar] (미국 텍사스슈퍼컴퓨팅센터 선임연구원)
**5. Yoonhee Ko (2012.8-2014.2), currently Associate Professor at [https://hufsbiomed.weebly.com/ Department of Biomedical Engineering, Hankuk University of Foreign Studies], Korea [https://scholar.google.com/citations?user=GBxCYX8AAAAJ&hl=en Google Scholar] (한국외국어대 바이오공학과 교수)
**6. Jonghoon Lee (2013.10-2014.2), currently Professor at [https://www.gachon.ac.kr/foodbiotech/6142/subview.do Department of Food Biotechnology, Gachon University], Korea (가천대학교 식품생명공학과 교수)
**7. Jung Eun Shim (2009.8-2017.11), currently Staff Scientist at Yonsei Genomics Center Bioinformatics Data Analysis Core (연세의료원 유전체센터 생명정보분석코어 책임연구원)

*'''Former Graduate Students (Ph.D)'''
**1. Junha Shin (2008.9-2014.2), PhD; currently Scientist at [https://wid.wisc.edu/people/junha-shin/ Wisconsin Institute for Discovery], USA (미국 위스콘신 대학연구소 연구원)
**2. Hanhae Kim (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**3. Ara Cho (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**4. Eiru Kim (2010.9-2016.8), PhD; currently Senior Expert in Data Science, [https://www.gnf.org/ The Genomics Institute of the Novartis Research Foundation], San Diego, USA (노바티스 선임데이터분석연구원)
**5. Tak Lee (2011.3-2017.2), PhD; currently Senior Bioinformatician, [https://www.mpipz.mpg.de/en Max Planck Institute for Plant Breeding Research] (독일 막스플랭크 연구소 선임생명정보학자)
**6. Heonjong Han (2013.3~2019.8), PhD; currently Bioinformatics engineer at [https://3billion.io/ 3billion] (바이오기업 데이터사이언티스트)
**7. Kyungsoo Kim (2013.3~2020.2), PhD; currently Research Professor at Severance Hospital (강남세브란스의료원 유방암센터 연구교수)
**8. Jae-Won Cho (2016.9~2021.2), PhD; currently Assistant Professor at [https://ibb.hanyang.ac.kr/ Hanyang Institute of Bioscience and Biotechnology] (한양대학교 한양생명과학기술원 조교수)
**9. Chan Yeong Kim (2015.3~2021.2), PhD; currently Postdoc Fellow at European Molecular Biology Laboratory in Heidelberg [http://www.bork.embl.de/j/ Bork Group] (유럽연합분자생물학연구소 박사후 연구원)
**10. Sungho Lee (2017.3-2024.2), PhD; currently Data Scientist at [http://www.mogam.re.kr/kor/ MOGAM Institute for Biomedical Research] (목암생명과학연구소, (주)녹십자 출연 연구소, 선임연구원)
**11. Junha Cha (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://dna-discovery.stanford.edu/ Prof. Hanlee P. Ji Lab](미국 스탠퍼드대학교 박사후연구원)
**12. Seungbyn Baek (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://kundajelab.github.io/ Prof. Anshul Kundaje Lab](미국 스탠퍼드대학교 박사후연구원)
**13. Nayeon Kim (2019.9-2025.2), PhD; currently Postdoc Fellow at KAIST InnoCORE Research Group (과학기술원 InnoCORE 초거대언어모델 혁신 연구단, 박사후연구원)

*'''Former Graduate Students (Master's degree)'''
**1. Sun-Gou Ji (2009.9-2011.8), M.Eng.; PhD from University of Cambridge (Sanger Genome center); currently Vice President, Computational Genetics at [https://bridgebio.com/ BridgeBio Pharma], Boston, USA (미 바이오기업 부대표)
**2. Hyojin Kim (2013.3-2015.2), M.Eng.; PhD from University of Aachen; currently Scientist at Bayer, Germany [https://www.linkedin.com/in/hyojin-kim-b3bb711ab Linkedin] (독일 바이엘 제약회사 선임 연구원)
**3. Hongseok Shim (2013.9-2015.8), M.Eng.; currently PhD student, Arizona State University, Biomedical Informatics program (애리조나주립대 생물정보학 박사과정)
**4. Sunmo Yang (2014.9-2017.2), M.Eng. currently Bioinformatics programmer, Yonsei University (연세대 네트워크생명공학 연구실 책임데이터연구원)
**5. Muyoung Lee (2016.3-2018.2), M.Eng. currently PhD student, University of Texas at Austin, Cellular and Molecular Biology Program (텍사스주립대 생물정보학 박사과정)
**6. Jiwon Yu (2021.9-2023.8), M.Eng. currently Data Scientist at [https://www.samsungbioepis.com/kr/index.do SAMSUNG BIOEPIS] (삼성바이오에피스 데이터사이언티스트)
**7. Geon_Koh (2022.9-2025.2), M.Eng. currently Researcher at Gachon University, College of Medicine (가천의대 시스템생물학 연구실 연구원)
**8. Wonjong Kim (2023.3-2025.8), M.Eng. currently Researcher at [https://samsungbiologics.com/ SAMSUNG Biologics] (삼성바이오로직스 연구원)

*'''Former Visiting Scientists/Students'''
**1. Minkyung Shin (2012.3-2012.7), went to University of Southern California graduate school
**2. Paul Chung (2012 summer), currently work at [https://about.meta.com/ Meta], USA
**3. Hyunjin Cho (2014 summer), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA
**4. Michael Chung (2016.8-2016.12), currently work at [https://about.meta.com/ Meta], USA

*'''Former Undergraduate Students'''
**1. Ila Shin, went to medical school (Yonsei Univ.) Currently Professor, Kyunghee University School of Medicine (경희대학교 의과대학 교수)
**2. Yoonkyung Ko
**3. Sangyo Park, went to law school (Kyounghee Univ.)
**4. Jayoon Shin, went to medical school (Pusan National Univ.)
**5. Dongjoo Sun, went to dental school (Wongwang Univ.)
**6. Eulsoo Kim
**7. Myungwhan Lee, went to medical school (Yonsei Univ.)
**8. Moonhee Lee, went to graduate school (University of Amsterdam, Netherlands)
**9. Jinhyun Ju, went to graduate school (Cornell Medical School, Computational Systems Biology); Currently Principal Computational Biologist, Cancer Genomics at [https://bridgebio.com/ BridgeBio Pharma], Seattle, USA (미 바이오기업 선임연구원)
**10. Haeyoung Shin, went to graduate school (Brown University, Computational Neuroscience); Currently Professor, Seoul National University (서울대학교 생명과학부 교수)
**11. Joonghee Soh, went to graduate school (KAIST, Culture Technology)
**12. Hee Jung Cho, went to graduate school (UC Berkeley)
**13. TaeHwan Kim, went to medical school
**14. Joohyung Kim, went to medical school (Kyungpook National Univ.)
**15. Donghyun Shin, went to medical school (Yonsei Univ.)
**16. Byunghee Kang (2015 spring - 2016 summer), went to graduate school (PosTech)
**17. Sunphil Kim (2016 winter)
**18. Jaeho Shim (2016 winter)
**19. Seunghyun Shin (2016 spring)
**20. Aejoo Hong (2016 spring)
**21. Changbae Bang (2016 summer), went to medical school (Yonsei Univ.)
**22. Seoyoung Choi (2016 summer)
**23. Dabin Jung (2016 summer)
**24. Boreum Nam (2016 summer)
**25. Seungun Lee (2016 summer)
**26. Yeaji Kim (2016 summer and fall)
**27. Sangyoung Lee (2017 winter)
**28. Heejun Jang (2017 winter & spring), went to KIST as Research Assistant
**29. Jungha Lee (2017 summer), went to graduate school (Seoul National Univ.)
**30. Seunghyun Wang (2017 summer), went to graduate school (KAIST)
**31. Dong-Min Yang (2017 fall)
**32. Doo-Hee Lee (2017 fall)
**33. Suk-Jae Han (2018 winter)
**34. Ji-Eun Han (2018 winter)
**35. Yuri Ko (2018 spring)
**36. Sung-Woo Kim (2018 spring)
**37. Woosung Kwon (2018 summer)
**38. Soyun Kong (2018 summer)
**39. Hojeong Keum (2018 summer and fall)
**40. Sungjun Lim (2018 summer and fall)
**41. Jiyoon Lee (2018 summer and fall)
**42. Ilseok Choi(2019 winter, spring, summer and fall, 2020 winter, spring)
**43. Junik Park (2019 winter)
**44. Lee Yoo (2019 winter & spring)
**45. Yeonwha Kim (2019 winter & spring)
**46. Sohee Kim (2019 spring)
**47. Juseong Lee (2019 spring)
**48. Junyoung Yang (2019 spring & summer)
**49. Junyeong Ma (2019 summer, 2020 winter, summer, fall, 2021 winter)
**50. Dayeon Jung (2019 summer)
**51. Hanjoon Kim (2019 summer, 2021 winter)
**52. Hyungjin Kim (2020 winter, spring)
**53. Sujin Hyun (2020 winter)
**54. Hyuki Lee (2020 winter)
**55. Donghwan Lee (2020 winter)
**56. Jun Hyung Cha (2020 spring, summer)
**57. Jiwon Yu (2020 summer, 2021 Spring, summer)
**58. Dong Seok Kim (2020 summer)
**59. Donggeun Lee (2020 summer)
**60. Sehun Ahn (2020 summer, 2021 winter, spring, summer, 2022 winter)
**61. Jiho Kim (2020 summer)
**62. Euijung Seong (2020 fall, 2021 spring, summer)
**63. Junhan Kim (2021 winter & spring)
**64. Suyong Choi (2021 winter)
**65. Sujin Pyeon (2021 Spring)
**66. Hyeon Hee Ji (2021 Spring)
**67. Semin Kim (2021 Summer)
**68. Su Hwan Kim (2021 Summer)
**69. Yongbin Kim (2021 Summer)
**70. Nan Park (2021 Summer)
**71. Hoyong Jung (2021 Summer)
**72. Ingyeong Koh (2021 Summer)
**73. Jongbin Jeong (2022 Winter)
**74. Sungchul Yang (2022 Winter, Spring, Summer)
**75. Hyojung Lee (2022 Winter, Spring)
**76. Jun Hyeong Kim (2022 Winter, Spring)
**77. Young Ji Roh (2022 Spring, Summer)
**78. Geon Koh (2022 Spring, Summer)
**79. Hayoung Kang (2022 Summer, 2023 Spring)
**80. Won Jong Kim (2022 Summer, Fall, 2023 Winter)
**81. Christian Lee (2022 Summer)
**82. Je Yun Kang (2022 Summer)
**83. Sumin Lee (2022 Fall)
**84. Jungyeon Kim (2022 Fall, 2023 Winter)
**85. Seol Song (2023 Winter)
**86. Soyeon Kim (2023 Summer)
**87. Sieun Park (2023 Summer)
**88. Gunhyeong Lee (2023 Summer)
**89. Yunseo Han (2023 Summer)
**90. Jae Hyun Kim (2023 Summer)
**91. Jeong-min Seo (2023 Summer)
**92. Yerin Kim (2023 Fall, 2024 Winter)
**93. Sang Min Park (2024 Winter)
**94. Minsun Seo (2024 Winter)
**95. Jaeryun Sim (2024 Winter)
**96. Sun Min Lim (2024 Winter)
**97. Yurim Jung (2024 Spring, Summer)
**98. Hae Been Lee (2024 Spring, Summer)
**99. Zunu An (2024 Summer, Fall, 2025 Winter, Spring, Summer)
**100. Se Bin Lim (2024 Summer, Fall, 2025 Winter)
**101. Sang Min Yoon (2024 Summer)
**102. Yena Kim (2024 Summer)
**103. Kang Eon Lee (2024 Fall)
**104. Soyoon Park (2025 Winter)
**105. Sojung Lee (2025 Winter)
**106. Leanne Ma (2025 Winter)
**107. Seung Wan Jeon (2025 Summer)
**108. Joongun Lee (2025 Summer)
**109. Minseo Kim (2025 Summer)
**110. Hong Kyu Park (2025 Summer)
**111. Yunyeong Jang (2025 Fall, 2026 Winter)
**112. Jong Hyun Hwang (2025 Fall, 2026 Winter)
**113. Gyuweon Park (2025 Fall)

People

2025-12-04T08:37:51Z

Il1001: /* Undergraduate Students */

__NOTOC__
=='''Scientists & Research Staff'''==
{|border="0" width="1080"
|align="center"|[[File:prof_Insuk_fixed.png|100px|link=people:IS_Lee]]
|align="center"|[[File:SM_fixed.png|100px|link=people:SM_Yang]]
|align="center"|[[File:Ilseok_fixed.png|100px|link=People:IS_Choi]]
|align="center"|[[File:JunHyeong_fixed.png|100px|link=People:Jun_Hyung_Cha]]
|align="center"|[[File:JunYeong_fixed.png|100px|link=People:Junyeong_Ma]]
|align="center"|[[File:Hanjune_fixed.png|100px|link=People:Han-June_KIM]]
|align="center"|[[File:EuiJeong_fixed.png|100px|link=People:EuiJeong_Sung]]
|-

|width=160px; align="center"|[[people:IS_Lee|<big>'''Insuk Lee'''</big>]]
|width=160px; align="center"|[[people:SM_Yang|<big>'''Sunmo Yang'''</big>]]
|width=160px; align="center"|[[People:IS_Choi|<big>'''Ilseok Choi'''</big>]]
|width=160px; align="center"|[[People:Jun_Hyung_Cha|<big>'''Jun Hyung Cha'''</big>]]
|width=160px; align="center"|[[People:Junyeong_Ma|<big>'''Junyeong Ma'''</big>]]
|width=160px; align="center"|[[People:Hanjune_Kim|<big>'''Hanjune Kim'''</big>]]
|width=160px; align="center"|[[People:Euijeong_Sung|<big>'''Euijeong Sung'''</big>]]
|-

|align="center"|[[people:IS_Lee|Principal Investigator Professor]]
|align="center"|[[people:SM_Yang|Bioinformatics Programmer & Sys. Admin]]
|align="center"|[[People:IS_Choi|Ph.D candidate (Single-cell Biology) (2020.9 - )]]
|align="center"|[[People:Jun_Hyung_Cha|Ph.D candidate (Microbiome) (2020.9 - )]]
|align="center"|[[People:Junyeong_Ma|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Hanjune_Kim|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Euijeong_Sung|Ph.D candidate (Single-cell Biology) (2021.9 - )]]
|}
{|border="0" width="1080"

|align="center"|[[File:Sehun_fixed.png|100px|link=People:Sehun_Ahn]]
|align="center"|[[File:Jungyeon_fixed.png|100px|link=People:Jungyeon_Kim]]
|align="center"|[[File:Yerin_fixed.png|100px|link=People:Yerin_Kim]]
|align="center"|[[File:Yurim_fixed_(2).jpg|100px|link=People:Yurim_Jung]]
|align="center"|[[File:HaeBeen_fixed.jpg|100px|link=People:Hae_Been_lee]]
|align="center"|[[File:Sebin_fixed.jpg|100px|link=People:Sebin_Lim]]
|-
|width=160px; align="center"|[[People:Sehun_Ahn|<big>'''Sehun Ahn'''</big>]]
|width=160px; align="center"|[[People:Jungyeon_Kim|<big>'''Jungyeon Kim'''</big>]]
|width=160px; align="center"|[[People:Yerin_Kim|<big>'''Yerin Kim'''</big>]]
|width=160px; align="center"|[[People:Yurim_Jung|<big>'''Yurim Jung'''</big>]]
|width=160px; align="center"|[[People:Hae_Been_lee|<big>'''Hae Been Lee'''</big>]]
|width=160px; align="center"|[[People:Sebin_Lim|<big>'''Sebin Lim'''</big>]]
|-
|align="center"|[[People:Sehun_Ahn|Ph.D candidate (Microbiome) (2022.3 - )]]
|align="center"|[[People:Jungyeon_Kim|Integrated Ph.D course (Microbiome) (2023.3 - )]]
|align="center"|[[People:Yerin_Kim|Integrated Ph.D course (Microbiome) (2024.3 - )]]
|align="center"|[[People:Yurim_Jung|Integrated Ph.D course (Single-cell Biology) (2024.9 - )]]
|align="center"|[[People:Hae_Been_lee|Integrated Ph.D course (Microbiome) (2024.9 - )]]
|align="center"|[[People:Sebin_Lim|Integrated Ph.D course (Microbiome) (2025.3 - )]]
|}

=='''Administrative Assistant'''==

=='''Undergraduate Students'''==
*Zunu An
*Seung Wan Jeon
*Yunyeong Jang
*Jong Hyun Hwang
*Sung Min Kim
*Zixuan Guo
*Hyeonjin Kim
*Eunjeong Kim

=='''Alumni'''==
*'''Former Post-docs and Staff Scientists'''
**1. Taeyun Oh (2009.5-2011.12), currently Senior Researcher at Cowellbiogim, Korea
**2. Sohyun Hwang (2010.3-2015.8), currently Professor at [https://grad.cha.ac.kr/%ed%99%a9%ec%86%8c%ed%98%84/ Department of Biomedical Science, CHA University], Korea [https://scholar.google.com/citations?user=z5yC9cwAAAAJ&hl=en Google Scholar] (차의과대학 의과학과 교수)
**3. Samuel Beck (2011.2-2011.12), currently Associate Professor at Boston University, USA, [https://beck310.wixsite.com/becklab Lab Homepage] (미 보스턴 대학교 부교수)
**4. Jawon Song (2011.1-2012.5), currently Research Associate at [https://www.tacc.utexas.edu/about/directory/jawon-song Texas Advanced Computing Center], Austin, TX, USA [https://scholar.google.com/citations?user=wv61wGoAAAAJ&hl=en Google Scholar] (미국 텍사스슈퍼컴퓨팅센터 선임연구원)
**5. Yoonhee Ko (2012.8-2014.2), currently Associate Professor at [https://hufsbiomed.weebly.com/ Department of Biomedical Engineering, Hankuk University of Foreign Studies], Korea [https://scholar.google.com/citations?user=GBxCYX8AAAAJ&hl=en Google Scholar] (한국외국어대 바이오공학과 교수)
**6. Jonghoon Lee (2013.10-2014.2), currently Professor at [https://www.gachon.ac.kr/foodbiotech/6142/subview.do Department of Food Biotechnology, Gachon University], Korea (가천대학교 식품생명공학과 교수)
**7. Jung Eun Shim (2009.8-2017.11), currently Staff Scientist at Yonsei Genomics Center Bioinformatics Data Analysis Core (연세의료원 유전체센터 생명정보분석코어 책임연구원)

*'''Former Graduate Students (Ph.D)'''
**1. Junha Shin (2008.9-2014.2), PhD; currently Scientist at [https://wid.wisc.edu/people/junha-shin/ Wisconsin Institute for Discovery], USA (미국 위스콘신 대학연구소 연구원)
**2. Hanhae Kim (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**3. Ara Cho (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**4. Eiru Kim (2010.9-2016.8), PhD; currently Senior Expert in Data Science, [https://www.gnf.org/ The Genomics Institute of the Novartis Research Foundation], San Diego, USA (노바티스 선임데이터분석연구원)
**5. Tak Lee (2011.3-2017.2), PhD; currently Senior Bioinformatician, [https://www.mpipz.mpg.de/en Max Planck Institute for Plant Breeding Research] (독일 막스플랭크 연구소 선임생명정보학자)
**6. Heonjong Han (2013.3~2019.8), PhD; currently Bioinformatics engineer at [https://3billion.io/ 3billion] (바이오기업 데이터사이언티스트)
**7. Kyungsoo Kim (2013.3~2020.2), PhD; currently Research Professor at Severance Hospital (강남세브란스의료원 유방암센터 연구교수)
**8. Jae-Won Cho (2016.9~2021.2), PhD; currently Assistant Professor at [https://ibb.hanyang.ac.kr/ Hanyang Institute of Bioscience and Biotechnology] (한양대학교 한양생명과학기술원 조교수)
**9. Chan Yeong Kim (2015.3~2021.2), PhD; currently Postdoc Fellow at European Molecular Biology Laboratory in Heidelberg [http://www.bork.embl.de/j/ Bork Group] (유럽연합분자생물학연구소 박사후 연구원)
**10. Sungho Lee (2017.3-2024.2), PhD; currently Data Scientist at [http://www.mogam.re.kr/kor/ MOGAM Institute for Biomedical Research] (목암생명과학연구소, (주)녹십자 출연 연구소, 선임연구원)
**11. Junha Cha (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://dna-discovery.stanford.edu/ Prof. Hanlee P. Ji Lab](미국 스탠퍼드대학교 박사후연구원)
**12. Seungbyn Baek (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://kundajelab.github.io/ Prof. Anshul Kundaje Lab](미국 스탠퍼드대학교 박사후연구원)
**13. Nayeon Kim (2019.9-2025.2), PhD; currently Postdoc Fellow at KAIST InnoCORE Research Group (과학기술원 InnoCORE 초거대언어모델 혁신 연구단, 박사후연구원)

*'''Former Graduate Students (Master's degree)'''
**1. Sun-Gou Ji (2009.9-2011.8), M.Eng.; PhD from University of Cambridge (Sanger Genome center); currently Vice President, Computational Genetics at [https://bridgebio.com/ BridgeBio Pharma], Boston, USA (미 바이오기업 부대표)
**2. Hyojin Kim (2013.3-2015.2), M.Eng.; PhD from University of Aachen; currently Scientist at Bayer, Germany [https://www.linkedin.com/in/hyojin-kim-b3bb711ab Linkedin] (독일 바이엘 제약회사 선임 연구원)
**3. Hongseok Shim (2013.9-2015.8), M.Eng.; currently PhD student, Arizona State University, Biomedical Informatics program (애리조나주립대 생물정보학 박사과정)
**4. Sunmo Yang (2014.9-2017.2), M.Eng. currently Bioinformatics programmer, Yonsei University (연세대 네트워크생명공학 연구실 책임데이터연구원)
**5. Muyoung Lee (2016.3-2018.2), M.Eng. currently PhD student, University of Texas at Austin, Cellular and Molecular Biology Program (텍사스주립대 생물정보학 박사과정)
**6. Jiwon Yu (2021.9-2023.8), M.Eng. currently Data Scientist at [https://www.samsungbioepis.com/kr/index.do SAMSUNG BIOEPIS] (삼성바이오에피스 데이터사이언티스트)
**7. Geon_Koh (2022.9-2025.2), M.Eng. currently Researcher at Gachon University, College of Medicine (가천의대 시스템생물학 연구실 연구원)
**8. Wonjong Kim (2023.3-2025.8), M.Eng. currently Researcher at [https://samsungbiologics.com/ SAMSUNG Biologics] (삼성바이오로직스 연구원)

*'''Former Visiting Scientists/Students'''
**1. Minkyung Shin (2012.3-2012.7), went to University of Southern California graduate school
**2. Paul Chung (2012 summer), currently work at [https://about.meta.com/ Meta], USA
**3. Hyunjin Cho (2014 summer), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA
**4. Michael Chung (2016.8-2016.12), currently work at [https://about.meta.com/ Meta], USA

*'''Former Undergraduate Students'''
**1. Ila Shin, went to medical school (Yonsei Univ.) Currently Professor, Kyunghee University School of Medicine (경희대학교 의과대학 교수)
**2. Yoonkyung Ko
**3. Sangyo Park, went to law school (Kyounghee Univ.)
**4. Jayoon Shin, went to medical school (Pusan National Univ.)
**5. Dongjoo Sun, went to dental school (Wongwang Univ.)
**6. Eulsoo Kim
**7. Myungwhan Lee, went to medical school (Yonsei Univ.)
**8. Moonhee Lee, went to graduate school (University of Amsterdam, Netherlands)
**9. Jinhyun Ju, went to graduate school (Cornell Medical School, Computational Systems Biology); Currently Principal Computational Biologist, Cancer Genomics at [https://bridgebio.com/ BridgeBio Pharma], Seattle, USA (미 바이오기업 선임연구원)
**10. Haeyoung Shin, went to graduate school (Brown University, Computational Neuroscience); Currently Professor, Seoul National University (서울대학교 생명과학부 교수)
**11. Joonghee Soh, went to graduate school (KAIST, Culture Technology)
**12. Hee Jung Cho, went to graduate school (UC Berkeley)
**13. TaeHwan Kim, went to medical school
**14. Joohyung Kim, went to medical school (Kyungpook National Univ.)
**15. Donghyun Shin, went to medical school (Yonsei Univ.)
**16. Byunghee Kang (2015 spring - 2016 summer), went to graduate school (PosTech)
**17. Sunphil Kim (2016 winter)
**18. Jaeho Shim (2016 winter)
**19. Seunghyun Shin (2016 spring)
**20. Aejoo Hong (2016 spring)
**21. Changbae Bang (2016 summer), went to medical school (Yonsei Univ.)
**22. Seoyoung Choi (2016 summer)
**23. Dabin Jung (2016 summer)
**24. Boreum Nam (2016 summer)
**25. Seungun Lee (2016 summer)
**26. Yeaji Kim (2016 summer and fall)
**27. Sangyoung Lee (2017 winter)
**28. Heejun Jang (2017 winter & spring), went to KIST as Research Assistant
**29. Jungha Lee (2017 summer), went to graduate school (Seoul National Univ.)
**30. Seunghyun Wang (2017 summer), went to graduate school (KAIST)
**31. Dong-Min Yang (2017 fall)
**32. Doo-Hee Lee (2017 fall)
**33. Suk-Jae Han (2018 winter)
**34. Ji-Eun Han (2018 winter)
**35. Yuri Ko (2018 spring)
**36. Sung-Woo Kim (2018 spring)
**37. Woosung Kwon (2018 summer)
**38. Soyun Kong (2018 summer)
**39. Hojeong Keum (2018 summer and fall)
**40. Sungjun Lim (2018 summer and fall)
**41. Jiyoon Lee (2018 summer and fall)
**42. Ilseok Choi(2019 winter, spring, summer and fall, 2020 winter, spring)
**43. Junik Park (2019 winter)
**44. Lee Yoo (2019 winter & spring)
**45. Yeonwha Kim (2019 winter & spring)
**46. Sohee Kim (2019 spring)
**47. Juseong Lee (2019 spring)
**48. Junyoung Yang (2019 spring & summer)
**49. Junyeong Ma (2019 summer, 2020 winter, summer, fall, 2021 winter)
**50. Dayeon Jung (2019 summer)
**51. Hanjoon Kim (2019 summer, 2021 winter)
**52. Hyungjin Kim (2020 winter, spring)
**53. Sujin Hyun (2020 winter)
**54. Hyuki Lee (2020 winter)
**55. Donghwan Lee (2020 winter)
**56. Jun Hyung Cha (2020 spring, summer)
**57. Jiwon Yu (2020 summer, 2021 Spring, summer)
**58. Dong Seok Kim (2020 summer)
**59. Donggeun Lee (2020 summer)
**60. Sehun Ahn (2020 summer, 2021 winter, spring, summer, 2022 winter)
**61. Jiho Kim (2020 summer)
**62. Euijung Seong (2020 fall, 2021 spring, summer)
**63. Junhan Kim (2021 winter & spring)
**64. Suyong Choi (2021 winter)
**65. Sujin Pyeon (2021 Spring)
**66. Hyeon Hee Ji (2021 Spring)
**67. Semin Kim (2021 Summer)
**68. Su Hwan Kim (2021 Summer)
**69. Yongbin Kim (2021 Summer)
**70. Nan Park (2021 Summer)
**71. Hoyong Jung (2021 Summer)
**72. Ingyeong Koh (2021 Summer)
**73. Jongbin Jeong (2022 Winter)
**74. Sungchul Yang (2022 Winter, Spring, Summer)
**75. Hyojung Lee (2022 Winter, Spring)
**76. Jun Hyeong Kim (2022 Winter, Spring)
**77. Young Ji Roh (2022 Spring, Summer)
**78. Geon Koh (2022 Spring, Summer)
**79. Hayoung Kang (2022 Summer, 2023 Spring)
**80. Won Jong Kim (2022 Summer, Fall, 2023 Winter)
**81. Christian Lee (2022 Summer)
**82. Je Yun Kang (2022 Summer)
**83. Sumin Lee (2022 Fall)
**84. Jungyeon Kim (2022 Fall, 2023 Winter)
**85. Seol Song (2023 Winter)
**86. Soyeon Kim (2023 Summer)
**87. Sieun Park (2023 Summer)
**88. Gunhyeong Lee (2023 Summer)
**89. Yunseo Han (2023 Summer)
**90. Jae Hyun Kim (2023 Summer)
**91. Jeong-min Seo (2023 Summer)
**92. Yerin Kim (2023 Fall, 2024 Winter)
**93. Sang Min Park (2024 Winter)
**94. Minsun Seo (2024 Winter)
**95. Jaeryun Sim (2024 Winter)
**96. Sun Min Lim (2024 Winter)
**97. Yurim Jung (2024 Spring, Summer)
**98. Hae Been Lee (2024 Spring, Summer)
**99. Zunu An (2024 Summer, Fall, 2025 Winter, Spring, Summer)
**100. Se Bin Lim (2024 Summer, Fall, 2025 Winter)
**101. Sang Min Yoon (2024 Summer)
**102. Yena Kim (2024 Summer)
**103. Kang Eon Lee (2024 Fall)
**104. Soyoon Park (2025 Winter)
**105. Sojung Lee (2025 Winter)
**106. Leanne Ma (2025 Winter)
**107. Seung Wan Jeon (2025 Summer)
**108. Joongun Lee (2025 Summer)
**109. Minseo Kim (2025 Summer)
**110. Hong Kyu Park (2025 Summer)
**111. Yunyeong Jang (2025 Fall, 2026 Winter)
**112. Jong Hyun Hwang (2025 Fall, 2026 Winter)
**113. Gyuweon Park (2025 Fall, 2026 Winter)

People

2025-11-26T13:52:40Z

Il1001:

__NOTOC__
=='''Scientists & Research Staff'''==
{|border="0" width="1080"
|align="center"|[[File:prof_Insuk_fixed.png|100px|link=people:IS_Lee]]
|align="center"|[[File:SM_fixed.png|100px|link=people:SM_Yang]]
|align="center"|[[File:Ilseok_fixed.png|100px|link=People:IS_Choi]]
|align="center"|[[File:JunHyeong_fixed.png|100px|link=People:Jun_Hyung_Cha]]
|align="center"|[[File:JunYeong_fixed.png|100px|link=People:Junyeong_Ma]]
|align="center"|[[File:Hanjune_fixed.png|100px|link=People:Han-June_KIM]]
|align="center"|[[File:EuiJeong_fixed.png|100px|link=People:EuiJeong_Sung]]
|-

|width=160px; align="center"|[[people:IS_Lee|<big>'''Insuk Lee'''</big>]]
|width=160px; align="center"|[[people:SM_Yang|<big>'''Sunmo Yang'''</big>]]
|width=160px; align="center"|[[People:IS_Choi|<big>'''Ilseok Choi'''</big>]]
|width=160px; align="center"|[[People:Jun_Hyung_Cha|<big>'''Jun Hyung Cha'''</big>]]
|width=160px; align="center"|[[People:Junyeong_Ma|<big>'''Junyeong Ma'''</big>]]
|width=160px; align="center"|[[People:Hanjune_Kim|<big>'''Hanjune Kim'''</big>]]
|width=160px; align="center"|[[People:Euijeong_Sung|<big>'''Euijeong Sung'''</big>]]
|-

|align="center"|[[people:IS_Lee|Principal Investigator Professor]]
|align="center"|[[people:SM_Yang|Bioinformatics Programmer & Sys. Admin]]
|align="center"|[[People:IS_Choi|Ph.D candidate (Single-cell Biology) (2020.9 - )]]
|align="center"|[[People:Jun_Hyung_Cha|Ph.D candidate (Microbiome) (2020.9 - )]]
|align="center"|[[People:Junyeong_Ma|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Hanjune_Kim|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Euijeong_Sung|Ph.D candidate (Single-cell Biology) (2021.9 - )]]
|}
{|border="0" width="1080"

|align="center"|[[File:Sehun_fixed.png|100px|link=People:Sehun_Ahn]]
|align="center"|[[File:Jungyeon_fixed.png|100px|link=People:Jungyeon_Kim]]
|align="center"|[[File:Yerin_fixed.png|100px|link=People:Yerin_Kim]]
|align="center"|[[File:Yurim_fixed_(2).jpg|100px|link=People:Yurim_Jung]]
|align="center"|[[File:HaeBeen_fixed.jpg|100px|link=People:Hae_Been_lee]]
|align="center"|[[File:Sebin_fixed.jpg|100px|link=People:Sebin_Lim]]
|-
|width=160px; align="center"|[[People:Sehun_Ahn|<big>'''Sehun Ahn'''</big>]]
|width=160px; align="center"|[[People:Jungyeon_Kim|<big>'''Jungyeon Kim'''</big>]]
|width=160px; align="center"|[[People:Yerin_Kim|<big>'''Yerin Kim'''</big>]]
|width=160px; align="center"|[[People:Yurim_Jung|<big>'''Yurim Jung'''</big>]]
|width=160px; align="center"|[[People:Hae_Been_lee|<big>'''Hae Been Lee'''</big>]]
|width=160px; align="center"|[[People:Sebin_Lim|<big>'''Sebin Lim'''</big>]]
|-
|align="center"|[[People:Sehun_Ahn|Ph.D candidate (Microbiome) (2022.3 - )]]
|align="center"|[[People:Jungyeon_Kim|Integrated Ph.D course (Microbiome) (2023.3 - )]]
|align="center"|[[People:Yerin_Kim|Integrated Ph.D course (Microbiome) (2024.3 - )]]
|align="center"|[[People:Yurim_Jung|Integrated Ph.D course (Single-cell Biology) (2024.9 - )]]
|align="center"|[[People:Hae_Been_lee|Integrated Ph.D course (Microbiome) (2024.9 - )]]
|align="center"|[[People:Sebin_Lim|Integrated Ph.D course (Microbiome) (2025.3 - )]]
|}

=='''Administrative Assistant'''==

=='''Undergraduate Students'''==
*Zunu An
*Seung Wan Jeon
*Yunyeong Jang
*Jong Hyun Hwang
*Gyuweon Park
*Sung Min Kim
*Zixuan Guo
*Hyeonjin Kim
*Eunjeong Kim

=='''Alumni'''==
*'''Former Post-docs and Staff Scientists'''
**1. Taeyun Oh (2009.5-2011.12), currently Senior Researcher at Cowellbiogim, Korea
**2. Sohyun Hwang (2010.3-2015.8), currently Professor at [https://grad.cha.ac.kr/%ed%99%a9%ec%86%8c%ed%98%84/ Department of Biomedical Science, CHA University], Korea [https://scholar.google.com/citations?user=z5yC9cwAAAAJ&hl=en Google Scholar] (차의과대학 의과학과 교수)
**3. Samuel Beck (2011.2-2011.12), currently Associate Professor at Boston University, USA, [https://beck310.wixsite.com/becklab Lab Homepage] (미 보스턴 대학교 부교수)
**4. Jawon Song (2011.1-2012.5), currently Research Associate at [https://www.tacc.utexas.edu/about/directory/jawon-song Texas Advanced Computing Center], Austin, TX, USA [https://scholar.google.com/citations?user=wv61wGoAAAAJ&hl=en Google Scholar] (미국 텍사스슈퍼컴퓨팅센터 선임연구원)
**5. Yoonhee Ko (2012.8-2014.2), currently Associate Professor at [https://hufsbiomed.weebly.com/ Department of Biomedical Engineering, Hankuk University of Foreign Studies], Korea [https://scholar.google.com/citations?user=GBxCYX8AAAAJ&hl=en Google Scholar] (한국외국어대 바이오공학과 교수)
**6. Jonghoon Lee (2013.10-2014.2), currently Professor at [https://www.gachon.ac.kr/foodbiotech/6142/subview.do Department of Food Biotechnology, Gachon University], Korea (가천대학교 식품생명공학과 교수)
**7. Jung Eun Shim (2009.8-2017.11), currently Staff Scientist at Yonsei Genomics Center Bioinformatics Data Analysis Core (연세의료원 유전체센터 생명정보분석코어 책임연구원)

*'''Former Graduate Students (Ph.D)'''
**1. Junha Shin (2008.9-2014.2), PhD; currently Scientist at [https://wid.wisc.edu/people/junha-shin/ Wisconsin Institute for Discovery], USA (미국 위스콘신 대학연구소 연구원)
**2. Hanhae Kim (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**3. Ara Cho (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**4. Eiru Kim (2010.9-2016.8), PhD; currently Senior Expert in Data Science, [https://www.gnf.org/ The Genomics Institute of the Novartis Research Foundation], San Diego, USA (노바티스 선임데이터분석연구원)
**5. Tak Lee (2011.3-2017.2), PhD; currently Senior Bioinformatician, [https://www.mpipz.mpg.de/en Max Planck Institute for Plant Breeding Research] (독일 막스플랭크 연구소 선임생명정보학자)
**6. Heonjong Han (2013.3~2019.8), PhD; currently Bioinformatics engineer at [https://3billion.io/ 3billion] (바이오기업 데이터사이언티스트)
**7. Kyungsoo Kim (2013.3~2020.2), PhD; currently Research Professor at Severance Hospital (강남세브란스의료원 유방암센터 연구교수)
**8. Jae-Won Cho (2016.9~2021.2), PhD; currently Assistant Professor at [https://ibb.hanyang.ac.kr/ Hanyang Institute of Bioscience and Biotechnology] (한양대학교 한양생명과학기술원 조교수)
**9. Chan Yeong Kim (2015.3~2021.2), PhD; currently Postdoc Fellow at European Molecular Biology Laboratory in Heidelberg [http://www.bork.embl.de/j/ Bork Group] (유럽연합분자생물학연구소 박사후 연구원)
**10. Sungho Lee (2017.3-2024.2), PhD; currently Data Scientist at [http://www.mogam.re.kr/kor/ MOGAM Institute for Biomedical Research] (목암생명과학연구소, (주)녹십자 출연 연구소, 선임연구원)
**11. Junha Cha (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://dna-discovery.stanford.edu/ Prof. Hanlee P. Ji Lab](미국 스탠퍼드대학교 박사후연구원)
**12. Seungbyn Baek (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://kundajelab.github.io/ Prof. Anshul Kundaje Lab](미국 스탠퍼드대학교 박사후연구원)
**13. Nayeon Kim (2019.9-2025.2), PhD; currently Postdoc Fellow at KAIST InnoCORE Research Group (과학기술원 InnoCORE 초거대언어모델 혁신 연구단, 박사후연구원)

*'''Former Graduate Students (Master's degree)'''
**1. Sun-Gou Ji (2009.9-2011.8), M.Eng.; PhD from University of Cambridge (Sanger Genome center); currently Vice President, Computational Genetics at [https://bridgebio.com/ BridgeBio Pharma], Boston, USA (미 바이오기업 부대표)
**2. Hyojin Kim (2013.3-2015.2), M.Eng.; PhD from University of Aachen; currently Scientist at Bayer, Germany [https://www.linkedin.com/in/hyojin-kim-b3bb711ab Linkedin] (독일 바이엘 제약회사 선임 연구원)
**3. Hongseok Shim (2013.9-2015.8), M.Eng.; currently PhD student, Arizona State University, Biomedical Informatics program (애리조나주립대 생물정보학 박사과정)
**4. Sunmo Yang (2014.9-2017.2), M.Eng. currently Bioinformatics programmer, Yonsei University (연세대 네트워크생명공학 연구실 책임데이터연구원)
**5. Muyoung Lee (2016.3-2018.2), M.Eng. currently PhD student, University of Texas at Austin, Cellular and Molecular Biology Program (텍사스주립대 생물정보학 박사과정)
**6. Jiwon Yu (2021.9-2023.8), M.Eng. currently Data Scientist at [https://www.samsungbioepis.com/kr/index.do SAMSUNG BIOEPIS] (삼성바이오에피스 데이터사이언티스트)
**7. Geon_Koh (2022.9-2025.2), M.Eng. currently Researcher at Gachon University, College of Medicine (가천의대 시스템생물학 연구실 연구원)
**8. Wonjong Kim (2023.3-2025.8), M.Eng. currently Researcher at [https://samsungbiologics.com/ SAMSUNG Biologics] (삼성바이오로직스 연구원)

*'''Former Visiting Scientists/Students'''
**1. Minkyung Shin (2012.3-2012.7), went to University of Southern California graduate school
**2. Paul Chung (2012 summer), currently work at [https://about.meta.com/ Meta], USA
**3. Hyunjin Cho (2014 summer), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA
**4. Michael Chung (2016.8-2016.12), currently work at [https://about.meta.com/ Meta], USA

*'''Former Undergraduate Students'''
**1. Ila Shin, went to medical school (Yonsei Univ.) Currently Professor, Kyunghee University School of Medicine (경희대학교 의과대학 교수)
**2. Yoonkyung Ko
**3. Sangyo Park, went to law school (Kyounghee Univ.)
**4. Jayoon Shin, went to medical school (Pusan National Univ.)
**5. Dongjoo Sun, went to dental school (Wongwang Univ.)
**6. Eulsoo Kim
**7. Myungwhan Lee, went to medical school (Yonsei Univ.)
**8. Moonhee Lee, went to graduate school (University of Amsterdam, Netherlands)
**9. Jinhyun Ju, went to graduate school (Cornell Medical School, Computational Systems Biology); Currently Principal Computational Biologist, Cancer Genomics at [https://bridgebio.com/ BridgeBio Pharma], Seattle, USA (미 바이오기업 선임연구원)
**10. Haeyoung Shin, went to graduate school (Brown University, Computational Neuroscience); Currently Professor, Seoul National University (서울대학교 생명과학부 교수)
**11. Joonghee Soh, went to graduate school (KAIST, Culture Technology)
**12. Hee Jung Cho, went to graduate school (UC Berkeley)
**13. TaeHwan Kim, went to medical school
**14. Joohyung Kim, went to medical school (Kyungpook National Univ.)
**15. Donghyun Shin, went to medical school (Yonsei Univ.)
**16. Byunghee Kang (2015 spring - 2016 summer), went to graduate school (PosTech)
**17. Sunphil Kim (2016 winter)
**18. Jaeho Shim (2016 winter)
**19. Seunghyun Shin (2016 spring)
**20. Aejoo Hong (2016 spring)
**21. Changbae Bang (2016 summer), went to medical school (Yonsei Univ.)
**22. Seoyoung Choi (2016 summer)
**23. Dabin Jung (2016 summer)
**24. Boreum Nam (2016 summer)
**25. Seungun Lee (2016 summer)
**26. Yeaji Kim (2016 summer and fall)
**27. Sangyoung Lee (2017 winter)
**28. Heejun Jang (2017 winter & spring), went to KIST as Research Assistant
**29. Jungha Lee (2017 summer), went to graduate school (Seoul National Univ.)
**30. Seunghyun Wang (2017 summer), went to graduate school (KAIST)
**31. Dong-Min Yang (2017 fall)
**32. Doo-Hee Lee (2017 fall)
**33. Suk-Jae Han (2018 winter)
**34. Ji-Eun Han (2018 winter)
**35. Yuri Ko (2018 spring)
**36. Sung-Woo Kim (2018 spring)
**37. Woosung Kwon (2018 summer)
**38. Soyun Kong (2018 summer)
**39. Hojeong Keum (2018 summer and fall)
**40. Sungjun Lim (2018 summer and fall)
**41. Jiyoon Lee (2018 summer and fall)
**42. Ilseok Choi(2019 winter, spring, summer and fall, 2020 winter, spring)
**43. Junik Park (2019 winter)
**44. Lee Yoo (2019 winter & spring)
**45. Yeonwha Kim (2019 winter & spring)
**46. Sohee Kim (2019 spring)
**47. Juseong Lee (2019 spring)
**48. Junyoung Yang (2019 spring & summer)
**49. Junyeong Ma (2019 summer, 2020 winter, summer, fall, 2021 winter)
**50. Dayeon Jung (2019 summer)
**51. Hanjoon Kim (2019 summer, 2021 winter)
**52. Hyungjin Kim (2020 winter, spring)
**53. Sujin Hyun (2020 winter)
**54. Hyuki Lee (2020 winter)
**55. Donghwan Lee (2020 winter)
**56. Jun Hyung Cha (2020 spring, summer)
**57. Jiwon Yu (2020 summer, 2021 Spring, summer)
**58. Dong Seok Kim (2020 summer)
**59. Donggeun Lee (2020 summer)
**60. Sehun Ahn (2020 summer, 2021 winter, spring, summer, 2022 winter)
**61. Jiho Kim (2020 summer)
**62. Euijung Seong (2020 fall, 2021 spring, summer)
**63. Junhan Kim (2021 winter & spring)
**64. Suyong Choi (2021 winter)
**65. Sujin Pyeon (2021 Spring)
**66. Hyeon Hee Ji (2021 Spring)
**67. Semin Kim (2021 Summer)
**68. Su Hwan Kim (2021 Summer)
**69. Yongbin Kim (2021 Summer)
**70. Nan Park (2021 Summer)
**71. Hoyong Jung (2021 Summer)
**72. Ingyeong Koh (2021 Summer)
**73. Jongbin Jeong (2022 Winter)
**74. Sungchul Yang (2022 Winter, Spring, Summer)
**75. Hyojung Lee (2022 Winter, Spring)
**76. Jun Hyeong Kim (2022 Winter, Spring)
**77. Young Ji Roh (2022 Spring, Summer)
**78. Geon Koh (2022 Spring, Summer)
**79. Hayoung Kang (2022 Summer, 2023 Spring)
**80. Won Jong Kim (2022 Summer, Fall, 2023 Winter)
**81. Christian Lee (2022 Summer)
**82. Je Yun Kang (2022 Summer)
**83. Sumin Lee (2022 Fall)
**84. Jungyeon Kim (2022 Fall, 2023 Winter)
**85. Seol Song (2023 Winter)
**86. Soyeon Kim (2023 Summer)
**87. Sieun Park (2023 Summer)
**88. Gunhyeong Lee (2023 Summer)
**89. Yunseo Han (2023 Summer)
**90. Jae Hyun Kim (2023 Summer)
**91. Jeong-min Seo (2023 Summer)
**92. Yerin Kim (2023 Fall, 2024 Winter)
**93. Sang Min Park (2024 Winter)
**94. Minsun Seo (2024 Winter)
**95. Jaeryun Sim (2024 Winter)
**96. Sun Min Lim (2024 Winter)
**97. Yurim Jung (2024 Spring, Summer)
**98. Hae Been Lee (2024 Spring, Summer)
**99. Zunu An (2024 Summer, Fall, 2025 Winter, Spring, Summer)
**100. Se Bin Lim (2024 Summer, Fall, 2025 Winter)
**101. Sang Min Yoon (2024 Summer)
**102. Yena Kim (2024 Summer)
**103. Kang Eon Lee (2024 Fall)
**104. Soyoon Park (2025 Winter)
**105. Sojung Lee (2025 Winter)
**106. Leanne Ma (2025 Winter)
**107. Seung Wan Jeon (2025 Summer)
**108. Joongun Lee (2025 Summer)
**109. Minseo Kim (2025 Summer)
**110. Hong Kyu Park (2025 Summer)
**111. Yunyeong Jang (2025 Fall, 2026 Winter)
**112. Jong Hyun Hwang (2025 Fall, 2026 Winter)
**113. Gyuweon Park (2025 Fall, 2026 Winter)

Publications

2025-11-25T02:29:20Z

Il1001: /* 2024 (11) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (2)==
*130. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Review'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
==2025 (12)==
*128. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' Accepted [https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 July 7;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2025-11-25T02:23:22Z

Il1001: /* 2024 (11) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (2)==
*130. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Review'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
==2025 (12)==
*128. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' Accepted [https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Sep 10:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*114. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*113. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*112. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*111. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 Jan-Dec;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

People

2025-11-20T11:46:27Z

Il1001: /* Undergraduate Students */

__NOTOC__
=='''Scientists & Research Staff'''==
{|border="0" width="1080"
|align="center"|[[File:prof_Insuk_fixed.png|100px|link=people:IS_Lee]]
|align="center"|[[File:SM_fixed.png|100px|link=people:SM_Yang]]
|align="center"|[[File:Nayeon_fixed.png|100px|link=People:NY_Kim]]
|align="center"|[[File:Ilseok_fixed.png|100px|link=People:IS_Choi]]
|align="center"|[[File:JunHyeong_fixed.png|100px|link=People:Jun_Hyung_Cha]]
|align="center"|[[File:JunYeong_fixed.png|100px|link=People:Junyeong_Ma]]
|align="center"|[[File:Hanjune_fixed.png|100px|link=People:Han-June_KIM]]
|-

|width=160px; align="center"|[[people:IS_Lee|<big>'''Insuk Lee'''</big>]]
|width=160px; align="center"|[[people:SM_Yang|<big>'''Sunmo Yang'''</big>]]
|width=160px; align="center"|[[People:NY_Kim|<big>'''Nayeon Kim'''</big>]]
|width=160px; align="center"|[[People:IS_Choi|<big>'''Ilseok Choi'''</big>]]
|width=160px; align="center"|[[People:Jun_Hyung_Cha|<big>'''Jun Hyung Cha'''</big>]]
|width=160px; align="center"|[[People:Junyeong_Ma|<big>'''Junyeong Ma'''</big>]]
|width=160px; align="center"|[[People:Hanjune_Kim|<big>'''Hanjune Kim'''</big>]]
|-

|align="center"|[[people:IS_Lee|Principal Investigator Professor]]
|align="center"|[[people:SM_Yang|Bioinformatics Programmer & Sys. Admin]]
|align="center"|[[People:NY_Kim|Postdoc Fellow (Microbiome) ]]
|align="center"|[[People:IS_Choi|Ph.D candidate (Single-cell Biology) (2020.9 - )]]
|align="center"|[[People:Jun_Hyung_Cha|Ph.D candidate (Microbiome) (2020.9 - )]]
|align="center"|[[People:Junyeong_Ma|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Hanjune_Kim|Ph.D candidate (Microbiome) (2021.3 - )]]
|}
{|border="0" width="1080"

|align="center"|[[File:EuiJeong_fixed.png|100px|link=People:EuiJeong_Sung]]
|align="center"|[[File:Sehun_fixed.png|100px|link=People:Sehun_Ahn]]
|align="center"|[[File:Jungyeon_fixed.png|100px|link=People:Jungyeon_Kim]]
|align="center"|[[File:Yerin_fixed.png|100px|link=People:Yerin_Kim]]
|align="center"|[[File:Yurim_fixed_(2).jpg|100px|link=People:Yurim_Jung]]
|align="center"|[[File:HaeBeen_fixed.jpg|100px|link=People:Hae_Been_lee]]
|align="center"|[[File:Sebin_fixed.jpg|100px|link=People:Sebin_Lim]]
|-
|width=160px; align="center"|[[People:Euijeong_Sung|<big>'''Euijeong Sung'''</big>]]
|width=160px; align="center"|[[People:Sehun_Ahn|<big>'''Sehun Ahn'''</big>]]
|width=160px; align="center"|[[People:Jungyeon_Kim|<big>'''Jungyeon Kim'''</big>]]
|width=160px; align="center"|[[People:Yerin_Kim|<big>'''Yerin Kim'''</big>]]
|width=160px; align="center"|[[People:Yurim_Jung|<big>'''Yurim Jung'''</big>]]
|width=160px; align="center"|[[People:Hae_Been_lee|<big>'''Hae Been Lee'''</big>]]
|width=160px; align="center"|[[People:Sebin_Lim|<big>'''Sebin Lim'''</big>]]
|-
|align="center"|[[People:Euijeong_Sung|Ph.D candidate (Single-cell Biology) (2021.9 - )]]
|align="center"|[[People:Sehun_Ahn|Ph.D candidate (Microbiome) (2022.3 - )]]
|align="center"|[[People:Jungyeon_Kim|Integrated Ph.D course (Microbiome) (2023.3 - )]]
|align="center"|[[People:Yerin_Kim|Integrated Ph.D course (Microbiome) (2024.3 - )]]
|align="center"|[[People:Yurim_Jung|Integrated Ph.D course (Single-cell Biology) (2024.9 - )]]
|align="center"|[[People:Hae_Been_lee|Integrated Ph.D course (Microbiome) (2024.9 - )]]
|align="center"|[[People:Sebin_Lim|Integrated Ph.D course (Microbiome) (2025.3 - )]]
|}

=='''Administrative Assistant'''==

=='''Undergraduate Students'''==
*Zunu An
*Seung Wan Jeon
*Yunyeong Jang
*Jong Hyun Hwang
*Gyuweon Park
*Sung Min Kim
*Zixuan Guo
*Hyeonjin Kim
*Eunjeong Kim

=='''Alumni'''==
*'''Former Post-docs and Staff Scientists'''
**1. Taeyun Oh (2009.5-2011.12), currently Senior Researcher at Cowellbiogim, Korea
**2. Sohyun Hwang (2010.3-2015.8), currently Professor at [https://grad.cha.ac.kr/%ed%99%a9%ec%86%8c%ed%98%84/ Department of Biomedical Science, CHA University], Korea [https://scholar.google.com/citations?user=z5yC9cwAAAAJ&hl=en Google Scholar] (차의과대학 의과학과 교수)
**3. Samuel Beck (2011.2-2011.12), currently Associate Professor at Boston University, USA, [https://beck310.wixsite.com/becklab Lab Homepage] (미 보스턴 대학교 부교수)
**4. Jawon Song (2011.1-2012.5), currently Research Associate at [https://www.tacc.utexas.edu/about/directory/jawon-song Texas Advanced Computing Center], Austin, TX, USA [https://scholar.google.com/citations?user=wv61wGoAAAAJ&hl=en Google Scholar] (미국 텍사스슈퍼컴퓨팅센터 선임연구원)
**5. Yoonhee Ko (2012.8-2014.2), currently Associate Professor at [https://hufsbiomed.weebly.com/ Department of Biomedical Engineering, Hankuk University of Foreign Studies], Korea [https://scholar.google.com/citations?user=GBxCYX8AAAAJ&hl=en Google Scholar] (한국외국어대 바이오공학과 교수)
**6. Jonghoon Lee (2013.10-2014.2), currently Professor at [https://www.gachon.ac.kr/foodbiotech/6142/subview.do Department of Food Biotechnology, Gachon University], Korea (가천대학교 식품생명공학과 교수)
**7. Jung Eun Shim (2009.8-2017.11), currently Staff Scientist at Yonsei Genomics Center Bioinformatics Data Analysis Core (연세의료원 유전체센터 생명정보분석코어 책임연구원)

*'''Former Graduate Students (Ph.D)'''
**1. Junha Shin (2008.9-2014.2), PhD; currently Scientist at [https://wid.wisc.edu/people/junha-shin/ Wisconsin Institute for Discovery], USA (미국 위스콘신 대학연구소 연구원)
**2. Hanhae Kim (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**3. Ara Cho (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**4. Eiru Kim (2010.9-2016.8), PhD; currently Senior Expert in Data Science, [https://www.gnf.org/ The Genomics Institute of the Novartis Research Foundation], San Diego, USA (노바티스 선임데이터분석연구원)
**5. Tak Lee (2011.3-2017.2), PhD; currently Senior Bioinformatician, [https://www.mpipz.mpg.de/en Max Planck Institute for Plant Breeding Research] (독일 막스플랭크 연구소 선임생명정보학자)
**6. Heonjong Han (2013.3~2019.8), PhD; currently Bioinformatics engineer at [https://3billion.io/ 3billion] (바이오기업 데이터사이언티스트)
**7. Kyungsoo Kim (2013.3~2020.2), PhD; currently Research Professor at Severance Hospital (강남세브란스의료원 유방암센터 연구교수)
**8. Jae-Won Cho (2016.9~2021.2), PhD; currently Assistant Professor at [https://ibb.hanyang.ac.kr/ Hanyang Institute of Bioscience and Biotechnology] (한양대학교 한양생명과학기술원 조교수)
**9. Chan Yeong Kim (2015.3~2021.2), PhD; currently Postdoc Fellow at European Molecular Biology Laboratory in Heidelberg [http://www.bork.embl.de/j/ Bork Group] (유럽연합분자생물학연구소 박사후 연구원)
**10. Sungho Lee (2017.3-2024.2), PhD; currently Data Scientist at [http://www.mogam.re.kr/kor/ MOGAM Institute for Biomedical Research] (목암생명과학연구소, (주)녹십자 출연 연구소, 선임연구원)
**11. Junha Cha (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://dna-discovery.stanford.edu/ Prof. Hanlee P. Ji Lab](미국 스탠퍼드대학교 박사후연구원)
**12. Seungbyn Baek (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://kundajelab.github.io/ Prof. Anshul Kundaje Lab](미국 스탠퍼드대학교 박사후연구원)
**13. Nayeon Kim (2019.9-2025.2), PhD; currently Postdoc Fellow at KAIST InnoCORE Research Group (과학기술원 InnoCORE 초거대언어모델 혁신 연구단, 박사후연구원)

*'''Former Graduate Students (Master's degree)'''
**1. Sun-Gou Ji (2009.9-2011.8), M.Eng.; PhD from University of Cambridge (Sanger Genome center); currently Vice President, Computational Genetics at [https://bridgebio.com/ BridgeBio Pharma], Boston, USA (미 바이오기업 부대표)
**2. Hyojin Kim (2013.3-2015.2), M.Eng.; PhD from University of Aachen; currently Scientist at Bayer, Germany [https://www.linkedin.com/in/hyojin-kim-b3bb711ab Linkedin] (독일 바이엘 제약회사 선임 연구원)
**3. Hongseok Shim (2013.9-2015.8), M.Eng.; currently PhD student, Arizona State University, Biomedical Informatics program (애리조나주립대 생물정보학 박사과정)
**4. Sunmo Yang (2014.9-2017.2), M.Eng. currently Bioinformatics programmer, Yonsei University (연세대 네트워크생명공학 연구실 책임데이터연구원)
**5. Muyoung Lee (2016.3-2018.2), M.Eng. currently PhD student, University of Texas at Austin, Cellular and Molecular Biology Program (텍사스주립대 생물정보학 박사과정)
**6. Jiwon Yu (2021.9-2023.8), M.Eng. currently Data Scientist at [https://www.samsungbioepis.com/kr/index.do SAMSUNG BIOEPIS] (삼성바이오에피스 데이터사이언티스트)
**7. Geon_Koh (2022.9-2025.2), M.Eng. currently Researcher at Gachon University, College of Medicine (가천의대 시스템생물학 연구실 연구원)
**8. Wonjong Kim (2023.3-2025.8), M.Eng. currently Researcher at [https://samsungbiologics.com/ SAMSUNG Biologics] (삼성바이오로직스 연구원)

*'''Former Visiting Scientists/Students'''
**1. Minkyung Shin (2012.3-2012.7), went to University of Southern California graduate school
**2. Paul Chung (2012 summer), currently work at [https://about.meta.com/ Meta], USA
**3. Hyunjin Cho (2014 summer), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA
**4. Michael Chung (2016.8-2016.12), currently work at [https://about.meta.com/ Meta], USA

*'''Former Undergraduate Students'''
**1. Ila Shin, went to medical school (Yonsei Univ.) Currently Professor, Kyunghee University School of Medicine (경희대학교 의과대학 교수)
**2. Yoonkyung Ko
**3. Sangyo Park, went to law school (Kyounghee Univ.)
**4. Jayoon Shin, went to medical school (Pusan National Univ.)
**5. Dongjoo Sun, went to dental school (Wongwang Univ.)
**6. Eulsoo Kim
**7. Myungwhan Lee, went to medical school (Yonsei Univ.)
**8. Moonhee Lee, went to graduate school (University of Amsterdam, Netherlands)
**9. Jinhyun Ju, went to graduate school (Cornell Medical School, Computational Systems Biology); Currently Principal Computational Biologist, Cancer Genomics at [https://bridgebio.com/ BridgeBio Pharma], Seattle, USA (미 바이오기업 선임연구원)
**10. Haeyoung Shin, went to graduate school (Brown University, Computational Neuroscience); Currently Professor, Seoul National University (서울대학교 생명과학부 교수)
**11. Joonghee Soh, went to graduate school (KAIST, Culture Technology)
**12. Hee Jung Cho, went to graduate school (UC Berkeley)
**13. TaeHwan Kim, went to medical school
**14. Joohyung Kim, went to medical school (Kyungpook National Univ.)
**15. Donghyun Shin, went to medical school (Yonsei Univ.)
**16. Byunghee Kang (2015 spring - 2016 summer), went to graduate school (PosTech)
**17. Sunphil Kim (2016 winter)
**18. Jaeho Shim (2016 winter)
**19. Seunghyun Shin (2016 spring)
**20. Aejoo Hong (2016 spring)
**21. Changbae Bang (2016 summer), went to medical school (Yonsei Univ.)
**22. Seoyoung Choi (2016 summer)
**23. Dabin Jung (2016 summer)
**24. Boreum Nam (2016 summer)
**25. Seungun Lee (2016 summer)
**26. Yeaji Kim (2016 summer and fall)
**27. Sangyoung Lee (2017 winter)
**28. Heejun Jang (2017 winter & spring), went to KIST as Research Assistant
**29. Jungha Lee (2017 summer), went to graduate school (Seoul National Univ.)
**30. Seunghyun Wang (2017 summer), went to graduate school (KAIST)
**31. Dong-Min Yang (2017 fall)
**32. Doo-Hee Lee (2017 fall)
**33. Suk-Jae Han (2018 winter)
**34. Ji-Eun Han (2018 winter)
**35. Yuri Ko (2018 spring)
**36. Sung-Woo Kim (2018 spring)
**37. Woosung Kwon (2018 summer)
**38. Soyun Kong (2018 summer)
**39. Hojeong Keum (2018 summer and fall)
**40. Sungjun Lim (2018 summer and fall)
**41. Jiyoon Lee (2018 summer and fall)
**42. Ilseok Choi(2019 winter, spring, summer and fall, 2020 winter, spring)
**43. Junik Park (2019 winter)
**44. Lee Yoo (2019 winter & spring)
**45. Yeonwha Kim (2019 winter & spring)
**46. Sohee Kim (2019 spring)
**47. Juseong Lee (2019 spring)
**48. Junyoung Yang (2019 spring & summer)
**49. Junyeong Ma (2019 summer, 2020 winter, summer, fall, 2021 winter)
**50. Dayeon Jung (2019 summer)
**51. Hanjoon Kim (2019 summer, 2021 winter)
**52. Hyungjin Kim (2020 winter, spring)
**53. Sujin Hyun (2020 winter)
**54. Hyuki Lee (2020 winter)
**55. Donghwan Lee (2020 winter)
**56. Jun Hyung Cha (2020 spring, summer)
**57. Jiwon Yu (2020 summer, 2021 Spring, summer)
**58. Dong Seok Kim (2020 summer)
**59. Donggeun Lee (2020 summer)
**60. Sehun Ahn (2020 summer, 2021 winter, spring, summer, 2022 winter)
**61. Jiho Kim (2020 summer)
**62. Euijung Seong (2020 fall, 2021 spring, summer)
**63. Junhan Kim (2021 winter & spring)
**64. Suyong Choi (2021 winter)
**65. Sujin Pyeon (2021 Spring)
**66. Hyeon Hee Ji (2021 Spring)
**67. Semin Kim (2021 Summer)
**68. Su Hwan Kim (2021 Summer)
**69. Yongbin Kim (2021 Summer)
**70. Nan Park (2021 Summer)
**71. Hoyong Jung (2021 Summer)
**72. Ingyeong Koh (2021 Summer)
**73. Jongbin Jeong (2022 Winter)
**74. Sungchul Yang (2022 Winter, Spring, Summer)
**75. Hyojung Lee (2022 Winter, Spring)
**76. Jun Hyeong Kim (2022 Winter, Spring)
**77. Young Ji Roh (2022 Spring, Summer)
**78. Geon Koh (2022 Spring, Summer)
**79. Hayoung Kang (2022 Summer, 2023 Spring)
**80. Won Jong Kim (2022 Summer, Fall, 2023 Winter)
**81. Christian Lee (2022 Summer)
**82. Je Yun Kang (2022 Summer)
**83. Sumin Lee (2022 Fall)
**84. Jungyeon Kim (2022 Fall, 2023 Winter)
**85. Seol Song (2023 Winter)
**86. Soyeon Kim (2023 Summer)
**87. Sieun Park (2023 Summer)
**88. Gunhyeong Lee (2023 Summer)
**89. Yunseo Han (2023 Summer)
**90. Jae Hyun Kim (2023 Summer)
**91. Jeong-min Seo (2023 Summer)
**92. Yerin Kim (2023 Fall, 2024 Winter)
**93. Sang Min Park (2024 Winter)
**94. Minsun Seo (2024 Winter)
**95. Jaeryun Sim (2024 Winter)
**96. Sun Min Lim (2024 Winter)
**97. Yurim Jung (2024 Spring, Summer)
**98. Hae Been Lee (2024 Spring, Summer)
**99. Zunu An (2024 Summer, Fall, 2025 Winter, Spring, Summer)
**100. Se Bin Lim (2024 Summer, Fall, 2025 Winter)
**101. Sang Min Yoon (2024 Summer)
**102. Yena Kim (2024 Summer)
**103. Kang Eon Lee (2024 Fall)
**104. Soyoon Park (2025 Winter)
**105. Sojung Lee (2025 Winter)
**106. Leanne Ma (2025 Winter)
**107. Seung Wan Jeon (2025 Summer)
**108. Joongun Lee (2025 Summer)
**109. Minseo Kim (2025 Summer)
**110. Hong Kyu Park (2025 Summer)
**111. Yunyeong Jang (2025 Fall, 2026 Winter)
**112. Jong Hyun Hwang (2025 Fall, 2026 Winter)
**113. Gyuweon Park (2025 Fall, 2026 Winter)

Publications

2025-11-20T06:04:28Z

Il1001: /* 2025 (12) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (2)==
*130. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Review'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
==2025 (12)==
*128. '''Jungyeon Kim*''', Nayeon Kim, Jun Hyung Cha, Junyeong Ma, and '''Insuk Lee**''', Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' Accepted [https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*114. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*113. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*112. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 Jan-Dec;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*111. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Jun 19:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2025-11-20T05:23:03Z

Il1001: /* 2025 (12) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (2)==
*130. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Review'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
==2025 (12)==
*128. Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' Accepted [https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:33(11):1977-1994.e8 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*114. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*113. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*112. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 Jan-Dec;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*111. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Jun 19:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2025-11-20T05:15:31Z

Il1001: /* 2025 (12) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (2)==
*130. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Review'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
==2025 (12)==
*128. Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' Accepted [https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772 [https://pubmed.ncbi.nlm.nih.gov/41244590/ pubmed]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:S1931-3128 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*114. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*113. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*112. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 Jan-Dec;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*111. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Jun 19:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

People

2025-11-17T01:52:45Z

Il1001: /* Undergraduate Students */

__NOTOC__
=='''Scientists & Research Staff'''==
{|border="0" width="1080"
|align="center"|[[File:prof_Insuk_fixed.png|100px|link=people:IS_Lee]]
|align="center"|[[File:SM_fixed.png|100px|link=people:SM_Yang]]
|align="center"|[[File:Nayeon_fixed.png|100px|link=People:NY_Kim]]
|align="center"|[[File:Ilseok_fixed.png|100px|link=People:IS_Choi]]
|align="center"|[[File:JunHyeong_fixed.png|100px|link=People:Jun_Hyung_Cha]]
|align="center"|[[File:JunYeong_fixed.png|100px|link=People:Junyeong_Ma]]
|align="center"|[[File:Hanjune_fixed.png|100px|link=People:Han-June_KIM]]
|-

|width=160px; align="center"|[[people:IS_Lee|<big>'''Insuk Lee'''</big>]]
|width=160px; align="center"|[[people:SM_Yang|<big>'''Sunmo Yang'''</big>]]
|width=160px; align="center"|[[People:NY_Kim|<big>'''Nayeon Kim'''</big>]]
|width=160px; align="center"|[[People:IS_Choi|<big>'''Ilseok Choi'''</big>]]
|width=160px; align="center"|[[People:Jun_Hyung_Cha|<big>'''Jun Hyung Cha'''</big>]]
|width=160px; align="center"|[[People:Junyeong_Ma|<big>'''Junyeong Ma'''</big>]]
|width=160px; align="center"|[[People:Hanjune_Kim|<big>'''Hanjune Kim'''</big>]]
|-

|align="center"|[[people:IS_Lee|Principal Investigator Professor]]
|align="center"|[[people:SM_Yang|Bioinformatics Programmer & Sys. Admin]]
|align="center"|[[People:NY_Kim|Postdoc Fellow (Microbiome) ]]
|align="center"|[[People:IS_Choi|Ph.D candidate (Single-cell Biology) (2020.9 - )]]
|align="center"|[[People:Jun_Hyung_Cha|Ph.D candidate (Microbiome) (2020.9 - )]]
|align="center"|[[People:Junyeong_Ma|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Hanjune_Kim|Ph.D candidate (Microbiome) (2021.3 - )]]
|}
{|border="0" width="1080"

|align="center"|[[File:EuiJeong_fixed.png|100px|link=People:EuiJeong_Sung]]
|align="center"|[[File:Sehun_fixed.png|100px|link=People:Sehun_Ahn]]
|align="center"|[[File:Jungyeon_fixed.png|100px|link=People:Jungyeon_Kim]]
|align="center"|[[File:Yerin_fixed.png|100px|link=People:Yerin_Kim]]
|align="center"|[[File:Yurim_fixed_(2).jpg|100px|link=People:Yurim_Jung]]
|align="center"|[[File:HaeBeen_fixed.jpg|100px|link=People:Hae_Been_lee]]
|align="center"|[[File:Sebin_fixed.jpg|100px|link=People:Sebin_Lim]]
|-
|width=160px; align="center"|[[People:Euijeong_Sung|<big>'''Euijeong Sung'''</big>]]
|width=160px; align="center"|[[People:Sehun_Ahn|<big>'''Sehun Ahn'''</big>]]
|width=160px; align="center"|[[People:Jungyeon_Kim|<big>'''Jungyeon Kim'''</big>]]
|width=160px; align="center"|[[People:Yerin_Kim|<big>'''Yerin Kim'''</big>]]
|width=160px; align="center"|[[People:Yurim_Jung|<big>'''Yurim Jung'''</big>]]
|width=160px; align="center"|[[People:Hae_Been_lee|<big>'''Hae Been Lee'''</big>]]
|width=160px; align="center"|[[People:Sebin_Lim|<big>'''Sebin Lim'''</big>]]
|-
|align="center"|[[People:Euijeong_Sung|Ph.D candidate (Single-cell Biology) (2021.9 - )]]
|align="center"|[[People:Sehun_Ahn|Ph.D candidate (Microbiome) (2022.3 - )]]
|align="center"|[[People:Jungyeon_Kim|Integrated Ph.D course (Microbiome) (2023.3 - )]]
|align="center"|[[People:Yerin_Kim|Integrated Ph.D course (Microbiome) (2024.3 - )]]
|align="center"|[[People:Yurim_Jung|Integrated Ph.D course (Single-cell Biology) (2024.9 - )]]
|align="center"|[[People:Hae_Been_lee|Integrated Ph.D course (Microbiome) (2024.9 - )]]
|align="center"|[[People:Sebin_Lim|Integrated Ph.D course (Microbiome) (2025.3 - )]]
|}

=='''Administrative Assistant'''==

=='''Undergraduate Students'''==
*Zunu An
*Seung Wan Jeon
*Yunyeong Jang
*Jong Hyun Hwang
*Gyuweon Park
*Sung Min Kim
*Zixuan Guo
*Hyeonjin Kim

=='''Alumni'''==
*'''Former Post-docs and Staff Scientists'''
**1. Taeyun Oh (2009.5-2011.12), currently Senior Researcher at Cowellbiogim, Korea
**2. Sohyun Hwang (2010.3-2015.8), currently Professor at [https://grad.cha.ac.kr/%ed%99%a9%ec%86%8c%ed%98%84/ Department of Biomedical Science, CHA University], Korea [https://scholar.google.com/citations?user=z5yC9cwAAAAJ&hl=en Google Scholar] (차의과대학 의과학과 교수)
**3. Samuel Beck (2011.2-2011.12), currently Associate Professor at Boston University, USA, [https://beck310.wixsite.com/becklab Lab Homepage] (미 보스턴 대학교 부교수)
**4. Jawon Song (2011.1-2012.5), currently Research Associate at [https://www.tacc.utexas.edu/about/directory/jawon-song Texas Advanced Computing Center], Austin, TX, USA [https://scholar.google.com/citations?user=wv61wGoAAAAJ&hl=en Google Scholar] (미국 텍사스슈퍼컴퓨팅센터 선임연구원)
**5. Yoonhee Ko (2012.8-2014.2), currently Associate Professor at [https://hufsbiomed.weebly.com/ Department of Biomedical Engineering, Hankuk University of Foreign Studies], Korea [https://scholar.google.com/citations?user=GBxCYX8AAAAJ&hl=en Google Scholar] (한국외국어대 바이오공학과 교수)
**6. Jonghoon Lee (2013.10-2014.2), currently Professor at [https://www.gachon.ac.kr/foodbiotech/6142/subview.do Department of Food Biotechnology, Gachon University], Korea (가천대학교 식품생명공학과 교수)
**7. Jung Eun Shim (2009.8-2017.11), currently Staff Scientist at Yonsei Genomics Center Bioinformatics Data Analysis Core (연세의료원 유전체센터 생명정보분석코어 책임연구원)

*'''Former Graduate Students (Ph.D)'''
**1. Junha Shin (2008.9-2014.2), PhD; currently Scientist at [https://wid.wisc.edu/people/junha-shin/ Wisconsin Institute for Discovery], USA (미국 위스콘신 대학연구소 연구원)
**2. Hanhae Kim (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**3. Ara Cho (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**4. Eiru Kim (2010.9-2016.8), PhD; currently Senior Expert in Data Science, [https://www.gnf.org/ The Genomics Institute of the Novartis Research Foundation], San Diego, USA (노바티스 선임데이터분석연구원)
**5. Tak Lee (2011.3-2017.2), PhD; currently Senior Bioinformatician, [https://www.mpipz.mpg.de/en Max Planck Institute for Plant Breeding Research] (독일 막스플랭크 연구소 선임생명정보학자)
**6. Heonjong Han (2013.3~2019.8), PhD; currently Bioinformatics engineer at [https://3billion.io/ 3billion] (바이오기업 데이터사이언티스트)
**7. Kyungsoo Kim (2013.3~2020.2), PhD; currently Research Professor at Severance Hospital (강남세브란스의료원 유방암센터 연구교수)
**8. Jae-Won Cho (2016.9~2021.2), PhD; currently Assistant Professor at [https://ibb.hanyang.ac.kr/ Hanyang Institute of Bioscience and Biotechnology] (한양대학교 한양생명과학기술원 조교수)
**9. Chan Yeong Kim (2015.3~2021.2), PhD; currently Postdoc Fellow at European Molecular Biology Laboratory in Heidelberg [http://www.bork.embl.de/j/ Bork Group] (유럽연합분자생물학연구소 박사후 연구원)
**10. Sungho Lee (2017.3-2024.2), PhD; currently Data Scientist at [http://www.mogam.re.kr/kor/ MOGAM Institute for Biomedical Research] (목암생명과학연구소, (주)녹십자 출연 연구소, 선임연구원)
**11. Junha Cha (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://dna-discovery.stanford.edu/ Prof. Hanlee P. Ji Lab](미국 스탠퍼드대학교 박사후연구원)
**12. Seungbyn Baek (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://kundajelab.github.io/ Prof. Anshul Kundaje Lab](미국 스탠퍼드대학교 박사후연구원)
**13. Nayeon Kim (2019.9-2025.2), PhD; currently Postdoc Fellow at KAIST InnoCORE Research Group (과학기술원 InnoCORE 초거대언어모델 혁신 연구단, 박사후연구원)

*'''Former Graduate Students (Master's degree)'''
**1. Sun-Gou Ji (2009.9-2011.8), M.Eng.; PhD from University of Cambridge (Sanger Genome center); currently Vice President, Computational Genetics at [https://bridgebio.com/ BridgeBio Pharma], Boston, USA (미 바이오기업 부대표)
**2. Hyojin Kim (2013.3-2015.2), M.Eng.; PhD from University of Aachen; currently Scientist at Bayer, Germany [https://www.linkedin.com/in/hyojin-kim-b3bb711ab Linkedin] (독일 바이엘 제약회사 선임 연구원)
**3. Hongseok Shim (2013.9-2015.8), M.Eng.; currently PhD student, Arizona State University, Biomedical Informatics program (애리조나주립대 생물정보학 박사과정)
**4. Sunmo Yang (2014.9-2017.2), M.Eng. currently Bioinformatics programmer, Yonsei University (연세대 네트워크생명공학 연구실 책임데이터연구원)
**5. Muyoung Lee (2016.3-2018.2), M.Eng. currently PhD student, University of Texas at Austin, Cellular and Molecular Biology Program (텍사스주립대 생물정보학 박사과정)
**6. Jiwon Yu (2021.9-2023.8), M.Eng. currently Data Scientist at [https://www.samsungbioepis.com/kr/index.do SAMSUNG BIOEPIS] (삼성바이오에피스 데이터사이언티스트)
**7. Geon_Koh (2022.9-2025.2), M.Eng. currently Researcher at Gachon University, College of Medicine (가천의대 시스템생물학 연구실 연구원)
**8. Wonjong Kim (2023.3-2025.8), M.Eng. currently Researcher at [https://samsungbiologics.com/ SAMSUNG Biologics] (삼성바이오로직스 연구원)

*'''Former Visiting Scientists/Students'''
**1. Minkyung Shin (2012.3-2012.7), went to University of Southern California graduate school
**2. Paul Chung (2012 summer), currently work at [https://about.meta.com/ Meta], USA
**3. Hyunjin Cho (2014 summer), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA
**4. Michael Chung (2016.8-2016.12), currently work at [https://about.meta.com/ Meta], USA

*'''Former Undergraduate Students'''
**1. Ila Shin, went to medical school (Yonsei Univ.) Currently Professor, Kyunghee University School of Medicine (경희대학교 의과대학 교수)
**2. Yoonkyung Ko
**3. Sangyo Park, went to law school (Kyounghee Univ.)
**4. Jayoon Shin, went to medical school (Pusan National Univ.)
**5. Dongjoo Sun, went to dental school (Wongwang Univ.)
**6. Eulsoo Kim
**7. Myungwhan Lee, went to medical school (Yonsei Univ.)
**8. Moonhee Lee, went to graduate school (University of Amsterdam, Netherlands)
**9. Jinhyun Ju, went to graduate school (Cornell Medical School, Computational Systems Biology); Currently Principal Computational Biologist, Cancer Genomics at [https://bridgebio.com/ BridgeBio Pharma], Seattle, USA (미 바이오기업 선임연구원)
**10. Haeyoung Shin, went to graduate school (Brown University, Computational Neuroscience); Currently Professor, Seoul National University (서울대학교 생명과학부 교수)
**11. Joonghee Soh, went to graduate school (KAIST, Culture Technology)
**12. Hee Jung Cho, went to graduate school (UC Berkeley)
**13. TaeHwan Kim, went to medical school
**14. Joohyung Kim, went to medical school (Kyungpook National Univ.)
**15. Donghyun Shin, went to medical school (Yonsei Univ.)
**16. Byunghee Kang (2015 spring - 2016 summer), went to graduate school (PosTech)
**17. Sunphil Kim (2016 winter)
**18. Jaeho Shim (2016 winter)
**19. Seunghyun Shin (2016 spring)
**20. Aejoo Hong (2016 spring)
**21. Changbae Bang (2016 summer), went to medical school (Yonsei Univ.)
**22. Seoyoung Choi (2016 summer)
**23. Dabin Jung (2016 summer)
**24. Boreum Nam (2016 summer)
**25. Seungun Lee (2016 summer)
**26. Yeaji Kim (2016 summer and fall)
**27. Sangyoung Lee (2017 winter)
**28. Heejun Jang (2017 winter & spring), went to KIST as Research Assistant
**29. Jungha Lee (2017 summer), went to graduate school (Seoul National Univ.)
**30. Seunghyun Wang (2017 summer), went to graduate school (KAIST)
**31. Dong-Min Yang (2017 fall)
**32. Doo-Hee Lee (2017 fall)
**33. Suk-Jae Han (2018 winter)
**34. Ji-Eun Han (2018 winter)
**35. Yuri Ko (2018 spring)
**36. Sung-Woo Kim (2018 spring)
**37. Woosung Kwon (2018 summer)
**38. Soyun Kong (2018 summer)
**39. Hojeong Keum (2018 summer and fall)
**40. Sungjun Lim (2018 summer and fall)
**41. Jiyoon Lee (2018 summer and fall)
**42. Ilseok Choi(2019 winter, spring, summer and fall, 2020 winter, spring)
**43. Junik Park (2019 winter)
**44. Lee Yoo (2019 winter & spring)
**45. Yeonwha Kim (2019 winter & spring)
**46. Sohee Kim (2019 spring)
**47. Juseong Lee (2019 spring)
**48. Junyoung Yang (2019 spring & summer)
**49. Junyeong Ma (2019 summer, 2020 winter, summer, fall, 2021 winter)
**50. Dayeon Jung (2019 summer)
**51. Hanjoon Kim (2019 summer, 2021 winter)
**52. Hyungjin Kim (2020 winter, spring)
**53. Sujin Hyun (2020 winter)
**54. Hyuki Lee (2020 winter)
**55. Donghwan Lee (2020 winter)
**56. Jun Hyung Cha (2020 spring, summer)
**57. Jiwon Yu (2020 summer, 2021 Spring, summer)
**58. Dong Seok Kim (2020 summer)
**59. Donggeun Lee (2020 summer)
**60. Sehun Ahn (2020 summer, 2021 winter, spring, summer, 2022 winter)
**61. Jiho Kim (2020 summer)
**62. Euijung Seong (2020 fall, 2021 spring, summer)
**63. Junhan Kim (2021 winter & spring)
**64. Suyong Choi (2021 winter)
**65. Sujin Pyeon (2021 Spring)
**66. Hyeon Hee Ji (2021 Spring)
**67. Semin Kim (2021 Summer)
**68. Su Hwan Kim (2021 Summer)
**69. Yongbin Kim (2021 Summer)
**70. Nan Park (2021 Summer)
**71. Hoyong Jung (2021 Summer)
**72. Ingyeong Koh (2021 Summer)
**73. Jongbin Jeong (2022 Winter)
**74. Sungchul Yang (2022 Winter, Spring, Summer)
**75. Hyojung Lee (2022 Winter, Spring)
**76. Jun Hyeong Kim (2022 Winter, Spring)
**77. Young Ji Roh (2022 Spring, Summer)
**78. Geon Koh (2022 Spring, Summer)
**79. Hayoung Kang (2022 Summer, 2023 Spring)
**80. Won Jong Kim (2022 Summer, Fall, 2023 Winter)
**81. Christian Lee (2022 Summer)
**82. Je Yun Kang (2022 Summer)
**83. Sumin Lee (2022 Fall)
**84. Jungyeon Kim (2022 Fall, 2023 Winter)
**85. Seol Song (2023 Winter)
**86. Soyeon Kim (2023 Summer)
**87. Sieun Park (2023 Summer)
**88. Gunhyeong Lee (2023 Summer)
**89. Yunseo Han (2023 Summer)
**90. Jae Hyun Kim (2023 Summer)
**91. Jeong-min Seo (2023 Summer)
**92. Yerin Kim (2023 Fall, 2024 Winter)
**93. Sang Min Park (2024 Winter)
**94. Minsun Seo (2024 Winter)
**95. Jaeryun Sim (2024 Winter)
**96. Sun Min Lim (2024 Winter)
**97. Yurim Jung (2024 Spring, Summer)
**98. Hae Been Lee (2024 Spring, Summer)
**99. Zunu An (2024 Summer, Fall, 2025 Winter, Spring, Summer)
**100. Se Bin Lim (2024 Summer, Fall, 2025 Winter)
**101. Sang Min Yoon (2024 Summer)
**102. Yena Kim (2024 Summer)
**103. Kang Eon Lee (2024 Fall)
**104. Soyoon Park (2025 Winter)
**105. Sojung Lee (2025 Winter)
**106. Leanne Ma (2025 Winter)
**107. Seung Wan Jeon (2025 Summer)
**108. Joongun Lee (2025 Summer)
**109. Minseo Kim (2025 Summer)
**110. Hong Kyu Park (2025 Summer)
**111. Yunyeong Jang (2025 Fall, 2026 Winter)
**112. Jong Hyun Hwang (2025 Fall, 2026 Winter)
**113. Gyuweon Park (2025 Fall, 2026 Winter)

Publications

2025-11-16T06:25:46Z

Il1001: /* 2025 (12) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (2)==
*130. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Review'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
==2025 (12)==
*128. Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 
*127. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' Accepted [https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 
*126. '''Zunu An*, Jun Hyung Cha*''', Kyu Ha Lee**, '''Insuk Lee**''', Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' 2025 Nov 21; 28(11):113772
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:S1931-3128 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*114. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*113. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*112. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 Jan-Dec;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*111. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Jun 19:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

Publications

2025-11-15T09:37:52Z

Il1001: /* 2025 (12) */

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
*[https://www.ibric.org/bric/hanbitsa/treatise.do?mode=author-treatise-list&srAuthorId=760 BRIC 한빛사논문]
*[https://yonsei.pure.elsevier.com/en/persons/in-suk-lee Yonsei University Researcher Portal]
*[https://pubmed.ncbi.nlm.nih.gov/?term=Insuk+Lee%5BAuthor%5D&sort=date Pubmed article list]
* '*' First authors; '**' Corresponding authors;
==2026 (2)==
*130. Shotgun Metagenomic Analysis of the Tongue-Coating Microbiome Reveals Oral Microbes and Their Functions in Older Adults with Dementia, '''''Under Review'''''
 
*129. Proteomic Profiling of Human Extracellular Vesicles Reveals Diagnostic Biomarkers for Colon Adenocarcinoma, '''''Under Revision'''''
 
==2025 (12)==
*128. Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery, '''''Under Revision'''''
 
*127. Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples, '''''iScience''''' Accepted
 
*126. '''Junyeong Ma*, Nayeon Kim*''', Jun Hyung Cha, Wonjong Kim, Chan Yeong Kim, Yong-ho Lee, Han Sang Kim, Yoon Dae Han, Dongeun Yong, Eugene Han, Sunmo Yang, Samuel Beck, '''Insuk Lee**''', A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models '''''Nature Microbiology''''' Accepted [https://www.biorxiv.org/content/10.1101/2024.12.11.627901v3 bioRxiv]
 
*125. '''Jun Hyung Cha*''', Nayeon Kim, Junyeong Ma, Sungho Lee, Geon Koh, Sunmo Yang, Samuel Beck, Iksu Byeon, Byunguk Lee, '''Insuk Lee**''', A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights, '''''Cell Host & Microbes''''' 2025 Nov 12:S1931-3128 [https://pubmed.ncbi.nlm.nih.gov/41167188/ pubmed] [https://www.biorxiv.org/content/10.1101/2025.03.10.642329v2 bioRxiv]
* Previewed by Cell Host & Microbes [https://www.cell.com/cell-host-microbe/abstract/S1931-3128(25)00423-8 Preview]
 
*124. '''Junha Cha*''', Chang Gon Kim*, Nam Suk Sim*, Gamin Kim, Wonrak Son, Dahee Kim, Yurim Jung, Hyun Jun Hong, Hae Been Lee, Jaehyung Kim, Jinna Kim, Sun Och Yoon, Seokhyeong Go, Jeongah Kim, Euijung Seong, Seungbyn Baek, Kyung Hwan Kim, Min Hee Hong**, Yoon Woo Koh**, '''Insuk Lee**''', Hye Ryun Kim**, 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy, '''''Cell Reports Medicine''''' 2025 Oct 21;6(10):102408 [https://pubmed.ncbi.nlm.nih.gov/41045934/ pubmed]
 
*123. '''Seungbyn Baek*''', Kyungwoo Song, and '''Insuk Lee**''', Single-cell Foundation Models: Bringing Artificial Intelligence into Cell Biology, '''''Experimental & Molecular Medicine''''' 2025 Oct 1;57(10):2169-2181 [https://pubmed.ncbi.nlm.nih.gov/41028523/ pubmed]
 
*122. '''Seungbyn Baek*''', Junha Cha, Min-Hee Hong, Gamin Kim, Yoon Woo Koh, Dahee Kim, Wonrak Son, Chan-Young Ock, Seungeun Lee, Martin Hemberg, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Comparative single-cell analysis of esophageal cancer subtypes reveals tumor microenvironment distinctions explaining varied immunotherapy responses '''''Cancer Communications''''' 2025 Sep 29;45(9):1194-1199 [https://pubmed.ncbi.nlm.nih.gov/40581834/ pubmed][https://www.biorxiv.org/content/10.1101/2024.09.24.614705v1 bioRxiv]
 
*121. '''Ilseok Choi*''', Kyung-A Kim*, Sang Cheol Kim*, Donghwan Park, Ki Taek Nam, Jun Hyung Cha, Seungbyn Baek, Junha Cha, Hye-Yeong Jo, Minsun Jung, Melody Y. Zeng, Irina Matei, Susan Bullman, Joong Bae Ahn, Yoon Dae Han**, Han Sang Kim**, '''Insuk Lee**''', Secretory IgA dysfunction underlies poor prognosis in Fusobacterium-infected colorectal cancer, '''''Gut Microbes''''' 2025 Jul 16;17(1):2528428 [https://pubmed.ncbi.nlm.nih.gov/40667611/ pubmed]
 
*120. '''Seungbyn Baek*''', Euijeong Sung, Gamin Kim, Min-Hee Hong, Chang Young Lee, Hyo Sup Shim, Seong Yong Park**, Hye Ryun Kim**, '''Insuk Lee**''', Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer '''''Cancer Communications''''' 2025 Apr;45(4):422-427 [https://pubmed.ncbi.nlm.nih.gov/39754710/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.09.24.614708v1 bioRxiv]
 
*119. '''Junha Cha**''' and '''Insuk Lee**''', Single-cell network biology enabling cell-type-resolved disease genetics, '''''Genomics & Informatics''''' 2025 Mar 27;23(1):10 [https://pubmed.ncbi.nlm.nih.gov/40148916/ pubmed]
 
*118. '''Euijeong Sung*''', Junha Cha, Seungbyn Baek, '''Insuk Lee**''', Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas '''''Animal Cells Systems''''' 2025 Mar 7;29(1):11-20 [https://pubmed.ncbi.nlm.nih.gov/40066175/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.12.12.628105v1 bioRxiv]
 
*117. '''Jiwon Yu*, Junha Cha*''', Geon Koh, '''Insuk Lee**''', HCNetlas: a reference database of human cell-type-specific gene networks to aid disease genetic analyses '''''PLoS Biology''''' 2025 Feb 5;23(2):e3002702, [https://pubmed.ncbi.nlm.nih.gov/39908239/ pubmed] [https://www.biorxiv.org/content/10.1101/2024.06.07.597878v1 bioRxiv]
 

==2024 (11)==
*116. '''Chan Yeong Kim*''', Dong Jin Park*, Beung Chul Ahn*, Seungbyn Baek, Min Hee Hong, Linh Thanh Nguyen, Sun Ha Hwang, Nayeon Kim, Daniel Podlesny, Askarbek Orakov, Christian Schudoma, Shahriyar Mahdi Robbani, Hyo Sup Shim, Hong In Yoon, Chang Young Lee, Seong Yong Park, Dongeun Yong, Mina Han, Peer Bork, Byoung Choul Kim**, Sang-Jun Ha**, Hye Ryun Kim**, '''Insuk Lee**''', A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy '''''Nature Communications''''' 2024 Dec 27;15:10726 [https://pubmed.ncbi.nlm.nih.gov/39730328/ PubMed]
 
*115. '''Nayeon Kim*''', Chan Yeong Kim, Junyeong Ma, Summo Yang, Dongjin Park, Sang-Jun Ha, and Peter Belenky**, '''Insuk Lee**''', MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes '''''Gut Microbes''''' 2024 Sept 4;16(1):2393791. [https://pubmed.ncbi.nlm.nih.gov/39230075/ PubMed]
 
*114. Daniel Chang*, Vinod K Gupta, Benjamin Hur, Sergio Cobo-López, Kevin Y Cunningham, Nam Soo Han, '''Insuk Lee''', Vanessa L Kronzer, Levi M Teigen, Lioudmila V Karnatovskaia, Erin E Longbrake, John M Davis III, Heidi Nelson, Jaeyun Sung** , Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles, '''''Nature Communications''''' 2024 Aug 28;15:7447 [https://pubmed.ncbi.nlm.nih.gov/39198444/ PubMed]
 
*113. '''Nayeon Kim*''', Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter Belenky** and '''Insuk Lee**''', Genome-Resolved Metagenomics: A Game Changer for Microbiome Medicine, '''''Experimental & Molecular Medicine''''' 2024 Jul 1;56(7):1501-1512. [https://pubmed.ncbi.nlm.nih.gov/38945961/ PubMed]
 
*112. '''Sungho Lee*''' and '''Insuk Lee**''', Comprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data '''''Gut Microbes''''' 2024 Jan-Dec;16(1):2375679 [https://pubmed.ncbi.nlm.nih.gov/38972064/ PubMed]
 
*111. Randall T. Mertens*, Aditya Misra*, Peng Xiao*, '''Seungbyn Baek''', Joseph M. Rone, Davide Mangani, Kisha N. Sivanathan, Adedamola S. Arojojoye, Samuel G. Awuah, '''Insuk Lee''', Guo-Ping Shi, Boryana Petrova, Jeannette R. Brook, Ana C. Anderson, Richard A. Flavell, Naama Kanarek, Martin Hemberg, Roni Nowarski**, A metabolic switch orchestrated by IL-18 and the cyclic dinucleotide cGAMP programs intestinal tolerance, '''''Immunity''''' 2024 Jun 19:S1074-7613(24)00305-4 [https://pubmed.ncbi.nlm.nih.gov/38906145/ PubMed]
 
*110. '''Junha Cha*''', Da Hee Kim*, Gamin Kim*, Jae-Won Cho, Euijeong Sung, Seungbyn Baek, Min Hee Hong, Chang Gon Kim, Nam Suk Sim, Hyun Jun Hong, Jung Eun Lee, Martin Hemberg, Seyeon Park, Sun Ock Yoon, Sang-Jun Ha**, Yoon Woo Koh**, Hye Ryun Kim**, and '''Insuk Lee**''', Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes, '''''Journal for Immunotherapy of Cancer'''''. 2024 Jun 10;12(6):e008667 [https://pubmed.ncbi.nlm.nih.gov/38857913/ PubMed]
 
*109. Chang Gon Kim*, Min Hee Hong*, Dahee Kim*, Brian Hyohyoung Lee*, Hyunwook Kim*, Chan-Young Ock*, Geoffrey Kelly, Yoon Ji Bang, Gamin Kim, Jung Eun Lee, Chaeyeon Kim, Se-Heon Kim, Hyun Jun Hong, Young Min Park, Nam Suk Sim, Heejung Park, Jin Woo Park, Chang Geol Lee, Kyung Hwan Kim, Goeun Park, Inkyung Jung, Dawoon Han, Jong Hoon Kim, '''Junha Cha''', '''Insuk Lee''', Mingu Kang, Heon Song, Chiyoon Oum, Seulki Kim, Sukjun Kim, Yoojoo Lim, Seunghee Kim-Schulze, Miriam Merad, Sun Och Yoon**, Hyun Je Kim**, Yoon Woo Koh**, Hye Ryun Kim**, A phase II open-label randomized clinical trial of preoperative durvalumab or durvalumab plus tremelimumab in resectable head and neck squamous cell carcinoma '''''Clinical Cancer Research''''' 2024 May 15;30(10):2097-2110 [https://pubmed.ncbi.nlm.nih.gov/38457288/ PubMed]
 
*108. Da Hyun Kim*, '''Sungho Lee*''', Jisong Ahn, Jae Hwan Kim, Eunjung Lee**, '''Insuk Lee**''', and Sanguine Byun**, Transcriptomic and metabolomic analysis unveils nanoplastic-induced gut barrier dysfunction via STAT1/6 and ERK pathways '''''Environmental Research''''' 2024 May 15:249:118437 [https://pubmed.ncbi.nlm.nih.gov/38346486/ PubMed]
 
*107. Critical Assessment of Genome Interpretation Consortium, CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods '''''Genome Biology''''' 2024 February 22;25(1):53 [https://pubmed.ncbi.nlm.nih.gov/38389099/ PubMed]
 
*106. Wei E Gordon*, '''Seungbyn Baek*''', Hai P Nguyen, Yien-Ming Kuo, Rachael Bradley, Sarah L. Fong, '''Nayeon Kim''', Alex Galazyuk, '''Insuk Lee''', Melissa Ingala, Nancy B Simmons, Tony Schountz, Lisa Cooper, Ilias Georgakopoulos-Soares, Martin Hemberg**, Nadav Ahituv**, Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas '''''Nature Communications''''' 2024 Jan 9;15(1):12 [https://pubmed.ncbi.nlm.nih.gov/38195585/ PubMed]
 

==2023 (3)==
*105. '''Junha Cha*''', Michael Lavi*, Junhan Kim, Noam Shomron**, '''Insuk Lee**''', Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis '''''Computational and Structural Biotechnology Journal''''' 2023 Mar 25;21:2296-2304 [https://pubmed.ncbi.nlm.nih.gov/37035549/ PubMed]
 
*104. '''Junha Cha*''', Jiwon Yu, Jae-Won Cho, Martin Hemberg**, '''Insuk Lee**''', scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes '''''Nucleic Acids Research''''' 2023 Jan 25;51(2):e8 [https://pubmed.ncbi.nlm.nih.gov/36350625/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.06.20.496836v1 bioRxiv]
 
*103. Myeong Joon Kim*, '''Kyungsoo Kim*''', Hyo Jin Park, Kyeong Hee Hong, Ji Hoon Oh, Jimin Son, '''Insuk Lee**''' and Sang-Jun Ha**, Deletion of PD-1 destabilizes the lineage identity and metabolic fitness of tumor-infiltrating regulatory T cells '''''Nature Immunology''''' 2023 Jan;24(1):148-161 [https://pubmed.ncbi.nlm.nih.gov/36577929/ PubMed]
 

==2022 (6)==
*102. '''Chan Yeong Kim*, Junyeong Ma*''', and '''Insuk Lee**''' HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota '''''Nature Communications''''' 2022 Oct 26;13(1):6367 [https://pubmed.ncbi.nlm.nih.gov/36289209/ PubMed] [https://www.biorxiv.org/content/10.1101/2022.02.09.479829v1 bioRxiv]
 
*101. '''Seungbyn Baek*''', Sunmo Yang, and '''Insuk Lee**''' COVID-GWAB: A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data '''''Biomolecules''''' 2022 Oct 12;12(10):1446 [https://pubmed.ncbi.nlm.nih.gov/36291657/ PubMed]
 
*100. Taeyun A Lee, '''Heonjong Han''', Ahsan Polash, Seok Keun Cho, Ji Won Lee, Eun A Ra, Eunhye Lee, Areum Park, Sujin Kang, Junhee L Choi, Ji Hyun Kim, Ji Eun Lee, Kyung-Won Min, Seong Wook Yang, Markus Hafner, '''Insuk Lee''', Je-Hyun Yoon, Sungwook Lee, Boyoun Park The nucleolus is the site for inflammatory RNA decay during infection '''''Nature Communications''''' 2022 Sep 3;13(1):5203 [https://pubmed.ncbi.nlm.nih.gov/36057640/ PubMed]
 
*99. Tae Gun Kang, Kee Woong Kwon, '''Kyungsoo Kim, Insuk Lee''', Myeong Joon Kim, Sang-Jun Ha, Sung Jae Shin Viral coinfection promotes tuberculosis immunopathogenesis by type I IFN signaling-dependent impediment of Th1 cell pulmonary influx, '''''Nature Communications''''' 2022 Jun 7;13(1):3155 [https://pubmed.ncbi.nlm.nih.gov/35672321/ PubMed]
 
*98. '''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. '''''Experimental & Molecular Medicine''''' 2022 Jan 5;54(1):12-22 [https://pubmed.ncbi.nlm.nih.gov/34987166/ PubMed] [//netbiolab.org/wiki/Cho_etal_2021_Table_S1-10.zip Supplementary Table S1-10]
 
*97. '''Chan Yeong Kim*, Seungbyn Baek*''', Junha Cha, Sunmo Yang, Eiru Kim, Edward M. Marcotte, Traver Hart, and '''Insuk Lee**''' HumanNet v3: An improved database of human gene networks for disease research '''''Nucleic Acids Research''''' 2022 Jan 7;50(D1):D632-D639 [https://pubmed.ncbi.nlm.nih.gov/34747468/ PubMed]
 

==2021 (5)==
*96. '''Jae-Won Cho*''', Seyeon Park, Gamin Kim, Heonjong Han, Hyo Sup Shim, Sunhye Shin, Yong-Soo Bae, '''Seong Yong Park** Sang-Jun Ha**, Insuk Lee**, Hye Ryun Kim**''' Dysregulation of T FH-B-T RM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer '''''Nature Communications''''' 2021 Oct 18;12(1):6068. [https://pubmed.ncbi.nlm.nih.gov/34663810/ PubMed]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2020 (9)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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] '''Recommended''' by [https://facultyopinions.com/prime/737459051 F1000]
 
*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]
 
*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]
 
*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]
 

==2019 (6)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2018 (5)==
*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]
 
*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]
 
*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]
 
*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]
 
*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]
 

==2017 (10)==
*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;
 
*70. '''Lee T*, Hwang S*''', Kim CY, Shim H, Kim H, Ronald P**, Marcotte E**, '''Lee I**''', WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum, '''''Molecular Plant.''''' 2017 Aug 7;10(8):1133-1136; [https://www.ncbi.nlm.nih.gov/pubmed/28450181 pubmed]
 
*69. '''Lee T*, Lee I**''', AraNet: A Network Biology Server for Arabidopsis thaliana and Other Non-Model Plant Species, '''''Methods in Molecular Biology''''' 2017 June 17; 1629:225-238; [https://www.ncbi.nlm.nih.gov/pubmed/28623589 pubmed]
 
*68. '''Shim JE*''', Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, '''Lee I**''', GWAB: a web server for the network-based boosting of human genome-wide association data, '''''Nucleic Acids Research''''' 2017 July 3; 45 (W1):W154-W161; [https://www.ncbi.nlm.nih.gov/pubmed/28449091 pubmed]
 
*67. '''Kim E*, Lee I**''', Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server, '''''Methods in Molecular Biology''''' 2017 April 28; 1611:183-198; [https://www.ncbi.nlm.nih.gov/pubmed/28451980 pubmed] [http://f1000.com/prime/727562216?bd=1 {{#widget:AddHtml|content=<img src="http://cdn.f1000.com.s3.amazonaws.com/images/badges/badgef1000.gif" alt="Access the recommendation on F1000Prime" id="bg" width=70 />}}]
 
*66. '''Shim JE*, Lee T*, Lee I**''', From sequencing data to gene functions: co-functional network approaches, '''''Animal Cells and Systems''''' 2017 April 15; 20:77-83; [https://www.ncbi.nlm.nih.gov/pubmed/30460054 pubmed]
 
*65. '''Kim H*''', Kim BS*, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS**, '''Lee I**''', TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits, '''''Molecular Plant.''''' 2017 April 3; 10:652–655; [https://www.ncbi.nlm.nih.gov/pubmed/27913317 pubmed]
 
*64. Jang K, Kim K, Cho A, '''Lee I''', Choi JK, Network perturbation by recurrent regulatory variants in cancer, '''''PLoS Compt. Biol.''''' 2017 Mar 23;13(3):e1005449; [https://www.ncbi.nlm.nih.gov/pubmed/28333928 pubmed]
 
*63. Yang S*, Kim CY, Hwang S, Kim E, Kim H, Shim H, '''Lee I**''', COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH), '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D389-D396 [https://www.ncbi.nlm.nih.gov/pubmed/27679477 pubmed]
 
*62. Kim E*, Hwang S, '''Lee I**''', SoyNet: a database of co-functional networks for soybean Glycine max, '''''Nucleic Acids Research''''' 2017 Jan 4; 45(D1):D1082-D1089. [http://www.ncbi.nlm.nih.gov/pubmed/27492285 pubmed]
 

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

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

==2014 (5)==
*37. '''Hwang S*''', Kim E, Yang S, Marcotte EM*, '''Lee I**''', MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, '''''Nucleic Acids Res''''' 2014 Jul;42(Web server issue):W147-53. [http://www.ncbi.nlm.nih.gov/pubmed/24861622 Pubmed]
 
*36. '''Lee I**''', A showcase of future plant biology: moving towards next-generation plant genetics assisted by genome sequencing and systems biology, '''''Genome Biology''''', 2014 May 23;15(5):305. [http://www.ncbi.nlm.nih.gov/pubmed/25001400 Pubmed]
 
*35. '''Cho A*''', Shin J, Hwang S, Kim C, Shim H, Kim H, Kim H, '''Lee I**''' WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, '''''Nucleic Acids Res'''''. 2014 Jul;42(Web Server issue):W76-82 [http://www.ncbi.nlm.nih.gov/pubmed/24813450 Pubmed]
 
*34. '''Shin J*''', Lee T, Kim H, '''Lee I**''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 2014 Jan;10(1):24-9 [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
 
*33. '''Kim H*''', Shin J, Kim E, Kim H, Hwang S, Shim JE, '''Lee I**''', YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. '''''Nucleic Acids Research''''' 2014 Jan;42(Database issue):D731-6 [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]
 

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

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

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

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

==2009 (3)==
*18. '''Lee I*''', Marcotte EM. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. 2009;541:463-75 [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]
 
*17. Li Z*, '''Lee I''', Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 2009 Oct;7(10):e1000213 [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]
 
*16. Gray RS, Abitua PB, Wlodarczyk BJ, Szabo-Rogers HL, Blanchard O, '''Lee I''', Weiss GS, Liu KJ, Marcotte EM, Wallingford JB, Finnell RH. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 2009 Oct;11(10):1225-32 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
 

==2008 (3)==
*15. Lehner B**, '''Lee I**''' . Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic'''''. 2008 May;7(3):217-27 '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]
 
*14. '''Lee I*''', Marcotte EM. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. 2008;453:267-78 [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]
 
*13. '''Lee I*''', Lehner B*, Crombie C, Wong W, Fraser AG, Marcotte EM. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 2008 Feb;40(2):181-8 '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
 

==Before 2007 (12)==
*12. '''Insuk Lee*''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]
 
*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]
 
*10. '''Insuk Lee*''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]
 
*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]
 
*8. '''Insuk Lee*''', Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]
 
*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]
 
*6. '''Insuk Lee*''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)
 
*5. '''Insuk Lee*''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)
 
*4. '''Insuk Lee*''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)
 
*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)
 
*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)
 
*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

People

2025-11-15T06:08:30Z

Il1001: /* Undergraduate Students */

__NOTOC__
=='''Scientists & Research Staff'''==
{|border="0" width="1080"
|align="center"|[[File:prof_Insuk_fixed.png|100px|link=people:IS_Lee]]
|align="center"|[[File:SM_fixed.png|100px|link=people:SM_Yang]]
|align="center"|[[File:Nayeon_fixed.png|100px|link=People:NY_Kim]]
|align="center"|[[File:Ilseok_fixed.png|100px|link=People:IS_Choi]]
|align="center"|[[File:JunHyeong_fixed.png|100px|link=People:Jun_Hyung_Cha]]
|align="center"|[[File:JunYeong_fixed.png|100px|link=People:Junyeong_Ma]]
|align="center"|[[File:Hanjune_fixed.png|100px|link=People:Han-June_KIM]]
|-

|width=160px; align="center"|[[people:IS_Lee|<big>'''Insuk Lee'''</big>]]
|width=160px; align="center"|[[people:SM_Yang|<big>'''Sunmo Yang'''</big>]]
|width=160px; align="center"|[[People:NY_Kim|<big>'''Nayeon Kim'''</big>]]
|width=160px; align="center"|[[People:IS_Choi|<big>'''Ilseok Choi'''</big>]]
|width=160px; align="center"|[[People:Jun_Hyung_Cha|<big>'''Jun Hyung Cha'''</big>]]
|width=160px; align="center"|[[People:Junyeong_Ma|<big>'''Junyeong Ma'''</big>]]
|width=160px; align="center"|[[People:Hanjune_Kim|<big>'''Hanjune Kim'''</big>]]
|-

|align="center"|[[people:IS_Lee|Principal Investigator Professor]]
|align="center"|[[people:SM_Yang|Bioinformatics Programmer & Sys. Admin]]
|align="center"|[[People:NY_Kim|Postdoc Fellow (Microbiome) ]]
|align="center"|[[People:IS_Choi|Ph.D candidate (Single-cell Biology) (2020.9 - )]]
|align="center"|[[People:Jun_Hyung_Cha|Ph.D candidate (Microbiome) (2020.9 - )]]
|align="center"|[[People:Junyeong_Ma|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Hanjune_Kim|Ph.D candidate (Microbiome) (2021.3 - )]]
|}
{|border="0" width="1080"

|align="center"|[[File:EuiJeong_fixed.png|100px|link=People:EuiJeong_Sung]]
|align="center"|[[File:Sehun_fixed.png|100px|link=People:Sehun_Ahn]]
|align="center"|[[File:Jungyeon_fixed.png|100px|link=People:Jungyeon_Kim]]
|align="center"|[[File:Yerin_fixed.png|100px|link=People:Yerin_Kim]]
|align="center"|[[File:Yurim_fixed_(2).jpg|100px|link=People:Yurim_Jung]]
|align="center"|[[File:HaeBeen_fixed.jpg|100px|link=People:Hae_Been_lee]]
|align="center"|[[File:Sebin_fixed.jpg|100px|link=People:Sebin_Lim]]
|-
|width=160px; align="center"|[[People:Euijeong_Sung|<big>'''Euijeong Sung'''</big>]]
|width=160px; align="center"|[[People:Sehun_Ahn|<big>'''Sehun Ahn'''</big>]]
|width=160px; align="center"|[[People:Jungyeon_Kim|<big>'''Jungyeon Kim'''</big>]]
|width=160px; align="center"|[[People:Yerin_Kim|<big>'''Yerin Kim'''</big>]]
|width=160px; align="center"|[[People:Yurim_Jung|<big>'''Yurim Jung'''</big>]]
|width=160px; align="center"|[[People:Hae_Been_lee|<big>'''Hae Been Lee'''</big>]]
|width=160px; align="center"|[[People:Sebin_Lim|<big>'''Sebin Lim'''</big>]]
|-
|align="center"|[[People:Euijeong_Sung|Ph.D candidate (Single-cell Biology) (2021.9 - )]]
|align="center"|[[People:Sehun_Ahn|Ph.D candidate (Microbiome) (2022.3 - )]]
|align="center"|[[People:Jungyeon_Kim|Integrated Ph.D course (Microbiome) (2023.3 - )]]
|align="center"|[[People:Yerin_Kim|Integrated Ph.D course (Microbiome) (2024.3 - )]]
|align="center"|[[People:Yurim_Jung|Integrated Ph.D course (Single-cell Biology) (2024.9 - )]]
|align="center"|[[People:Hae_Been_lee|Integrated Ph.D course (Microbiome) (2024.9 - )]]
|align="center"|[[People:Sebin_Lim|Integrated Ph.D course (Microbiome) (2025.3 - )]]
|}

=='''Administrative Assistant'''==

=='''Undergraduate Students'''==
*Zunu An
*Seung Wan Jeon
*Yunyeong Jang
*Jong Hyun Hwang
*Gyuweon Park
*Sung Min Kim
*Zixuan Guo

=='''Alumni'''==
*'''Former Post-docs and Staff Scientists'''
**1. Taeyun Oh (2009.5-2011.12), currently Senior Researcher at Cowellbiogim, Korea
**2. Sohyun Hwang (2010.3-2015.8), currently Professor at [https://grad.cha.ac.kr/%ed%99%a9%ec%86%8c%ed%98%84/ Department of Biomedical Science, CHA University], Korea [https://scholar.google.com/citations?user=z5yC9cwAAAAJ&hl=en Google Scholar] (차의과대학 의과학과 교수)
**3. Samuel Beck (2011.2-2011.12), currently Associate Professor at Boston University, USA, [https://beck310.wixsite.com/becklab Lab Homepage] (미 보스턴 대학교 부교수)
**4. Jawon Song (2011.1-2012.5), currently Research Associate at [https://www.tacc.utexas.edu/about/directory/jawon-song Texas Advanced Computing Center], Austin, TX, USA [https://scholar.google.com/citations?user=wv61wGoAAAAJ&hl=en Google Scholar] (미국 텍사스슈퍼컴퓨팅센터 선임연구원)
**5. Yoonhee Ko (2012.8-2014.2), currently Associate Professor at [https://hufsbiomed.weebly.com/ Department of Biomedical Engineering, Hankuk University of Foreign Studies], Korea [https://scholar.google.com/citations?user=GBxCYX8AAAAJ&hl=en Google Scholar] (한국외국어대 바이오공학과 교수)
**6. Jonghoon Lee (2013.10-2014.2), currently Professor at [https://www.gachon.ac.kr/foodbiotech/6142/subview.do Department of Food Biotechnology, Gachon University], Korea (가천대학교 식품생명공학과 교수)
**7. Jung Eun Shim (2009.8-2017.11), currently Staff Scientist at Yonsei Genomics Center Bioinformatics Data Analysis Core (연세의료원 유전체센터 생명정보분석코어 책임연구원)

*'''Former Graduate Students (Ph.D)'''
**1. Junha Shin (2008.9-2014.2), PhD; currently Scientist at [https://wid.wisc.edu/people/junha-shin/ Wisconsin Institute for Discovery], USA (미국 위스콘신 대학연구소 연구원)
**2. Hanhae Kim (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**3. Ara Cho (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**4. Eiru Kim (2010.9-2016.8), PhD; currently Senior Expert in Data Science, [https://www.gnf.org/ The Genomics Institute of the Novartis Research Foundation], San Diego, USA (노바티스 선임데이터분석연구원)
**5. Tak Lee (2011.3-2017.2), PhD; currently Senior Bioinformatician, [https://www.mpipz.mpg.de/en Max Planck Institute for Plant Breeding Research] (독일 막스플랭크 연구소 선임생명정보학자)
**6. Heonjong Han (2013.3~2019.8), PhD; currently Bioinformatics engineer at [https://3billion.io/ 3billion] (바이오기업 데이터사이언티스트)
**7. Kyungsoo Kim (2013.3~2020.2), PhD; currently Research Professor at Severance Hospital (강남세브란스의료원 유방암센터 연구교수)
**8. Jae-Won Cho (2016.9~2021.2), PhD; currently Assistant Professor at [https://ibb.hanyang.ac.kr/ Hanyang Institute of Bioscience and Biotechnology] (한양대학교 한양생명과학기술원 조교수)
**9. Chan Yeong Kim (2015.3~2021.2), PhD; currently Postdoc Fellow at European Molecular Biology Laboratory in Heidelberg [http://www.bork.embl.de/j/ Bork Group] (유럽연합분자생물학연구소 박사후 연구원)
**10. Sungho Lee (2017.3-2024.2), PhD; currently Data Scientist at [http://www.mogam.re.kr/kor/ MOGAM Institute for Biomedical Research] (목암생명과학연구소, (주)녹십자 출연 연구소, 선임연구원)
**11. Junha Cha (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://dna-discovery.stanford.edu/ Prof. Hanlee P. Ji Lab](미국 스탠퍼드대학교 박사후연구원)
**12. Seungbyn Baek (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://kundajelab.github.io/ Prof. Anshul Kundaje Lab](미국 스탠퍼드대학교 박사후연구원)
**13. Nayeon Kim (2019.9-2025.2), PhD; currently Postdoc Fellow at KAIST InnoCORE Research Group (과학기술원 InnoCORE 초거대언어모델 혁신 연구단, 박사후연구원)

*'''Former Graduate Students (Master's degree)'''
**1. Sun-Gou Ji (2009.9-2011.8), M.Eng.; PhD from University of Cambridge (Sanger Genome center); currently Vice President, Computational Genetics at [https://bridgebio.com/ BridgeBio Pharma], Boston, USA (미 바이오기업 부대표)
**2. Hyojin Kim (2013.3-2015.2), M.Eng.; PhD from University of Aachen; currently Scientist at Bayer, Germany [https://www.linkedin.com/in/hyojin-kim-b3bb711ab Linkedin] (독일 바이엘 제약회사 선임 연구원)
**3. Hongseok Shim (2013.9-2015.8), M.Eng.; currently PhD student, Arizona State University, Biomedical Informatics program (애리조나주립대 생물정보학 박사과정)
**4. Sunmo Yang (2014.9-2017.2), M.Eng. currently Bioinformatics programmer, Yonsei University (연세대 네트워크생명공학 연구실 책임데이터연구원)
**5. Muyoung Lee (2016.3-2018.2), M.Eng. currently PhD student, University of Texas at Austin, Cellular and Molecular Biology Program (텍사스주립대 생물정보학 박사과정)
**6. Jiwon Yu (2021.9-2023.8), M.Eng. currently Data Scientist at [https://www.samsungbioepis.com/kr/index.do SAMSUNG BIOEPIS] (삼성바이오에피스 데이터사이언티스트)
**7. Geon_Koh (2022.9-2025.2), M.Eng. currently Researcher at Gachon University, College of Medicine (가천의대 시스템생물학 연구실 연구원)
**8. Wonjong Kim (2023.3-2025.8), M.Eng. currently Researcher at [https://samsungbiologics.com/ SAMSUNG Biologics] (삼성바이오로직스 연구원)

*'''Former Visiting Scientists/Students'''
**1. Minkyung Shin (2012.3-2012.7), went to University of Southern California graduate school
**2. Paul Chung (2012 summer), currently work at [https://about.meta.com/ Meta], USA
**3. Hyunjin Cho (2014 summer), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA
**4. Michael Chung (2016.8-2016.12), currently work at [https://about.meta.com/ Meta], USA

*'''Former Undergraduate Students'''
**1. Ila Shin, went to medical school (Yonsei Univ.) Currently Professor, Kyunghee University School of Medicine (경희대학교 의과대학 교수)
**2. Yoonkyung Ko
**3. Sangyo Park, went to law school (Kyounghee Univ.)
**4. Jayoon Shin, went to medical school (Pusan National Univ.)
**5. Dongjoo Sun, went to dental school (Wongwang Univ.)
**6. Eulsoo Kim
**7. Myungwhan Lee, went to medical school (Yonsei Univ.)
**8. Moonhee Lee, went to graduate school (University of Amsterdam, Netherlands)
**9. Jinhyun Ju, went to graduate school (Cornell Medical School, Computational Systems Biology); Currently Principal Computational Biologist, Cancer Genomics at [https://bridgebio.com/ BridgeBio Pharma], Seattle, USA (미 바이오기업 선임연구원)
**10. Haeyoung Shin, went to graduate school (Brown University, Computational Neuroscience); Currently Professor, Seoul National University (서울대학교 생명과학부 교수)
**11. Joonghee Soh, went to graduate school (KAIST, Culture Technology)
**12. Hee Jung Cho, went to graduate school (UC Berkeley)
**13. TaeHwan Kim, went to medical school
**14. Joohyung Kim, went to medical school (Kyungpook National Univ.)
**15. Donghyun Shin, went to medical school (Yonsei Univ.)
**16. Byunghee Kang (2015 spring - 2016 summer), went to graduate school (PosTech)
**17. Sunphil Kim (2016 winter)
**18. Jaeho Shim (2016 winter)
**19. Seunghyun Shin (2016 spring)
**20. Aejoo Hong (2016 spring)
**21. Changbae Bang (2016 summer), went to medical school (Yonsei Univ.)
**22. Seoyoung Choi (2016 summer)
**23. Dabin Jung (2016 summer)
**24. Boreum Nam (2016 summer)
**25. Seungun Lee (2016 summer)
**26. Yeaji Kim (2016 summer and fall)
**27. Sangyoung Lee (2017 winter)
**28. Heejun Jang (2017 winter & spring), went to KIST as Research Assistant
**29. Jungha Lee (2017 summer), went to graduate school (Seoul National Univ.)
**30. Seunghyun Wang (2017 summer), went to graduate school (KAIST)
**31. Dong-Min Yang (2017 fall)
**32. Doo-Hee Lee (2017 fall)
**33. Suk-Jae Han (2018 winter)
**34. Ji-Eun Han (2018 winter)
**35. Yuri Ko (2018 spring)
**36. Sung-Woo Kim (2018 spring)
**37. Woosung Kwon (2018 summer)
**38. Soyun Kong (2018 summer)
**39. Hojeong Keum (2018 summer and fall)
**40. Sungjun Lim (2018 summer and fall)
**41. Jiyoon Lee (2018 summer and fall)
**42. Ilseok Choi(2019 winter, spring, summer and fall, 2020 winter, spring)
**43. Junik Park (2019 winter)
**44. Lee Yoo (2019 winter & spring)
**45. Yeonwha Kim (2019 winter & spring)
**46. Sohee Kim (2019 spring)
**47. Juseong Lee (2019 spring)
**48. Junyoung Yang (2019 spring & summer)
**49. Junyeong Ma (2019 summer, 2020 winter, summer, fall, 2021 winter)
**50. Dayeon Jung (2019 summer)
**51. Hanjoon Kim (2019 summer, 2021 winter)
**52. Hyungjin Kim (2020 winter, spring)
**53. Sujin Hyun (2020 winter)
**54. Hyuki Lee (2020 winter)
**55. Donghwan Lee (2020 winter)
**56. Jun Hyung Cha (2020 spring, summer)
**57. Jiwon Yu (2020 summer, 2021 Spring, summer)
**58. Dong Seok Kim (2020 summer)
**59. Donggeun Lee (2020 summer)
**60. Sehun Ahn (2020 summer, 2021 winter, spring, summer, 2022 winter)
**61. Jiho Kim (2020 summer)
**62. Euijung Seong (2020 fall, 2021 spring, summer)
**63. Junhan Kim (2021 winter & spring)
**64. Suyong Choi (2021 winter)
**65. Sujin Pyeon (2021 Spring)
**66. Hyeon Hee Ji (2021 Spring)
**67. Semin Kim (2021 Summer)
**68. Su Hwan Kim (2021 Summer)
**69. Yongbin Kim (2021 Summer)
**70. Nan Park (2021 Summer)
**71. Hoyong Jung (2021 Summer)
**72. Ingyeong Koh (2021 Summer)
**73. Jongbin Jeong (2022 Winter)
**74. Sungchul Yang (2022 Winter, Spring, Summer)
**75. Hyojung Lee (2022 Winter, Spring)
**76. Jun Hyeong Kim (2022 Winter, Spring)
**77. Young Ji Roh (2022 Spring, Summer)
**78. Geon Koh (2022 Spring, Summer)
**79. Hayoung Kang (2022 Summer, 2023 Spring)
**80. Won Jong Kim (2022 Summer, Fall, 2023 Winter)
**81. Christian Lee (2022 Summer)
**82. Je Yun Kang (2022 Summer)
**83. Sumin Lee (2022 Fall)
**84. Jungyeon Kim (2022 Fall, 2023 Winter)
**85. Seol Song (2023 Winter)
**86. Soyeon Kim (2023 Summer)
**87. Sieun Park (2023 Summer)
**88. Gunhyeong Lee (2023 Summer)
**89. Yunseo Han (2023 Summer)
**90. Jae Hyun Kim (2023 Summer)
**91. Jeong-min Seo (2023 Summer)
**92. Yerin Kim (2023 Fall, 2024 Winter)
**93. Sang Min Park (2024 Winter)
**94. Minsun Seo (2024 Winter)
**95. Jaeryun Sim (2024 Winter)
**96. Sun Min Lim (2024 Winter)
**97. Yurim Jung (2024 Spring, Summer)
**98. Hae Been Lee (2024 Spring, Summer)
**99. Zunu An (2024 Summer, Fall, 2025 Winter, Spring, Summer)
**100. Se Bin Lim (2024 Summer, Fall, 2025 Winter)
**101. Sang Min Yoon (2024 Summer)
**102. Yena Kim (2024 Summer)
**103. Kang Eon Lee (2024 Fall)
**104. Soyoon Park (2025 Winter)
**105. Sojung Lee (2025 Winter)
**106. Leanne Ma (2025 Winter)
**107. Seung Wan Jeon (2025 Summer)
**108. Joongun Lee (2025 Summer)
**109. Minseo Kim (2025 Summer)
**110. Hong Kyu Park (2025 Summer)
**111. Yunyeong Jang (2025 Fall, 2026 Winter)
**112. Jong Hyun Hwang (2025 Fall, 2026 Winter)
**113. Gyuweon Park (2025 Fall, 2026 Winter)

People

2025-11-15T06:07:04Z

Il1001:

__NOTOC__
=='''Scientists & Research Staff'''==
{|border="0" width="1080"
|align="center"|[[File:prof_Insuk_fixed.png|100px|link=people:IS_Lee]]
|align="center"|[[File:SM_fixed.png|100px|link=people:SM_Yang]]
|align="center"|[[File:Nayeon_fixed.png|100px|link=People:NY_Kim]]
|align="center"|[[File:Ilseok_fixed.png|100px|link=People:IS_Choi]]
|align="center"|[[File:JunHyeong_fixed.png|100px|link=People:Jun_Hyung_Cha]]
|align="center"|[[File:JunYeong_fixed.png|100px|link=People:Junyeong_Ma]]
|align="center"|[[File:Hanjune_fixed.png|100px|link=People:Han-June_KIM]]
|-

|width=160px; align="center"|[[people:IS_Lee|<big>'''Insuk Lee'''</big>]]
|width=160px; align="center"|[[people:SM_Yang|<big>'''Sunmo Yang'''</big>]]
|width=160px; align="center"|[[People:NY_Kim|<big>'''Nayeon Kim'''</big>]]
|width=160px; align="center"|[[People:IS_Choi|<big>'''Ilseok Choi'''</big>]]
|width=160px; align="center"|[[People:Jun_Hyung_Cha|<big>'''Jun Hyung Cha'''</big>]]
|width=160px; align="center"|[[People:Junyeong_Ma|<big>'''Junyeong Ma'''</big>]]
|width=160px; align="center"|[[People:Hanjune_Kim|<big>'''Hanjune Kim'''</big>]]
|-

|align="center"|[[people:IS_Lee|Principal Investigator Professor]]
|align="center"|[[people:SM_Yang|Bioinformatics Programmer & Sys. Admin]]
|align="center"|[[People:NY_Kim|Postdoc Fellow (Microbiome) ]]
|align="center"|[[People:IS_Choi|Ph.D candidate (Single-cell Biology) (2020.9 - )]]
|align="center"|[[People:Jun_Hyung_Cha|Ph.D candidate (Microbiome) (2020.9 - )]]
|align="center"|[[People:Junyeong_Ma|Ph.D candidate (Microbiome) (2021.3 - )]]
|align="center"|[[People:Hanjune_Kim|Ph.D candidate (Microbiome) (2021.3 - )]]
|}
{|border="0" width="1080"

|align="center"|[[File:EuiJeong_fixed.png|100px|link=People:EuiJeong_Sung]]
|align="center"|[[File:Sehun_fixed.png|100px|link=People:Sehun_Ahn]]
|align="center"|[[File:Jungyeon_fixed.png|100px|link=People:Jungyeon_Kim]]
|align="center"|[[File:Yerin_fixed.png|100px|link=People:Yerin_Kim]]
|align="center"|[[File:Yurim_fixed_(2).jpg|100px|link=People:Yurim_Jung]]
|align="center"|[[File:HaeBeen_fixed.jpg|100px|link=People:Hae_Been_lee]]
|align="center"|[[File:Sebin_fixed.jpg|100px|link=People:Sebin_Lim]]
|-
|width=160px; align="center"|[[People:Euijeong_Sung|<big>'''Euijeong Sung'''</big>]]
|width=160px; align="center"|[[People:Sehun_Ahn|<big>'''Sehun Ahn'''</big>]]
|width=160px; align="center"|[[People:Jungyeon_Kim|<big>'''Jungyeon Kim'''</big>]]
|width=160px; align="center"|[[People:Yerin_Kim|<big>'''Yerin Kim'''</big>]]
|width=160px; align="center"|[[People:Yurim_Jung|<big>'''Yurim Jung'''</big>]]
|width=160px; align="center"|[[People:Hae_Been_lee|<big>'''Hae Been Lee'''</big>]]
|width=160px; align="center"|[[People:Sebin_Lim|<big>'''Sebin Lim'''</big>]]
|-
|align="center"|[[People:Euijeong_Sung|Ph.D candidate (Single-cell Biology) (2021.9 - )]]
|align="center"|[[People:Sehun_Ahn|Ph.D candidate (Microbiome) (2022.3 - )]]
|align="center"|[[People:Jungyeon_Kim|Integrated Ph.D course (Microbiome) (2023.3 - )]]
|align="center"|[[People:Yerin_Kim|Integrated Ph.D course (Microbiome) (2024.3 - )]]
|align="center"|[[People:Yurim_Jung|Integrated Ph.D course (Single-cell Biology) (2024.9 - )]]
|align="center"|[[People:Hae_Been_lee|Integrated Ph.D course (Microbiome) (2024.9 - )]]
|align="center"|[[People:Sebin_Lim|Integrated Ph.D course (Microbiome) (2025.3 - )]]
|}

=='''Administrative Assistant'''==

=='''Undergraduate Students'''==
*Zunu An
*Seung Wan Jeon
*Yunyeong Jang
*Jong Hyun Hwang
*Gyuweon Park

=='''Alumni'''==
*'''Former Post-docs and Staff Scientists'''
**1. Taeyun Oh (2009.5-2011.12), currently Senior Researcher at Cowellbiogim, Korea
**2. Sohyun Hwang (2010.3-2015.8), currently Professor at [https://grad.cha.ac.kr/%ed%99%a9%ec%86%8c%ed%98%84/ Department of Biomedical Science, CHA University], Korea [https://scholar.google.com/citations?user=z5yC9cwAAAAJ&hl=en Google Scholar] (차의과대학 의과학과 교수)
**3. Samuel Beck (2011.2-2011.12), currently Associate Professor at Boston University, USA, [https://beck310.wixsite.com/becklab Lab Homepage] (미 보스턴 대학교 부교수)
**4. Jawon Song (2011.1-2012.5), currently Research Associate at [https://www.tacc.utexas.edu/about/directory/jawon-song Texas Advanced Computing Center], Austin, TX, USA [https://scholar.google.com/citations?user=wv61wGoAAAAJ&hl=en Google Scholar] (미국 텍사스슈퍼컴퓨팅센터 선임연구원)
**5. Yoonhee Ko (2012.8-2014.2), currently Associate Professor at [https://hufsbiomed.weebly.com/ Department of Biomedical Engineering, Hankuk University of Foreign Studies], Korea [https://scholar.google.com/citations?user=GBxCYX8AAAAJ&hl=en Google Scholar] (한국외국어대 바이오공학과 교수)
**6. Jonghoon Lee (2013.10-2014.2), currently Professor at [https://www.gachon.ac.kr/foodbiotech/6142/subview.do Department of Food Biotechnology, Gachon University], Korea (가천대학교 식품생명공학과 교수)
**7. Jung Eun Shim (2009.8-2017.11), currently Staff Scientist at Yonsei Genomics Center Bioinformatics Data Analysis Core (연세의료원 유전체센터 생명정보분석코어 책임연구원)

*'''Former Graduate Students (Ph.D)'''
**1. Junha Shin (2008.9-2014.2), PhD; currently Scientist at [https://wid.wisc.edu/people/junha-shin/ Wisconsin Institute for Discovery], USA (미국 위스콘신 대학연구소 연구원)
**2. Hanhae Kim (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**3. Ara Cho (2009.9-2015.2), PhD; currently Research Fellow at [http://www.kistep.re.kr Korea Institute of S&T Evaluation and Planning (KISTEP)] (한국과학기술기획평가원 연구위원)
**4. Eiru Kim (2010.9-2016.8), PhD; currently Senior Expert in Data Science, [https://www.gnf.org/ The Genomics Institute of the Novartis Research Foundation], San Diego, USA (노바티스 선임데이터분석연구원)
**5. Tak Lee (2011.3-2017.2), PhD; currently Senior Bioinformatician, [https://www.mpipz.mpg.de/en Max Planck Institute for Plant Breeding Research] (독일 막스플랭크 연구소 선임생명정보학자)
**6. Heonjong Han (2013.3~2019.8), PhD; currently Bioinformatics engineer at [https://3billion.io/ 3billion] (바이오기업 데이터사이언티스트)
**7. Kyungsoo Kim (2013.3~2020.2), PhD; currently Research Professor at Severance Hospital (강남세브란스의료원 유방암센터 연구교수)
**8. Jae-Won Cho (2016.9~2021.2), PhD; currently Assistant Professor at [https://ibb.hanyang.ac.kr/ Hanyang Institute of Bioscience and Biotechnology] (한양대학교 한양생명과학기술원 조교수)
**9. Chan Yeong Kim (2015.3~2021.2), PhD; currently Postdoc Fellow at European Molecular Biology Laboratory in Heidelberg [http://www.bork.embl.de/j/ Bork Group] (유럽연합분자생물학연구소 박사후 연구원)
**10. Sungho Lee (2017.3-2024.2), PhD; currently Data Scientist at [http://www.mogam.re.kr/kor/ MOGAM Institute for Biomedical Research] (목암생명과학연구소, (주)녹십자 출연 연구소, 선임연구원)
**11. Junha Cha (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://dna-discovery.stanford.edu/ Prof. Hanlee P. Ji Lab](미국 스탠퍼드대학교 박사후연구원)
**12. Seungbyn Baek (2019.9-2025.2), PhD; currently Postdoc Fellow at Stanford University, [https://kundajelab.github.io/ Prof. Anshul Kundaje Lab](미국 스탠퍼드대학교 박사후연구원)
**13. Nayeon Kim (2019.9-2025.2), PhD; currently Postdoc Fellow at KAIST InnoCORE Research Group (과학기술원 InnoCORE 초거대언어모델 혁신 연구단, 박사후연구원)

*'''Former Graduate Students (Master's degree)'''
**1. Sun-Gou Ji (2009.9-2011.8), M.Eng.; PhD from University of Cambridge (Sanger Genome center); currently Vice President, Computational Genetics at [https://bridgebio.com/ BridgeBio Pharma], Boston, USA (미 바이오기업 부대표)
**2. Hyojin Kim (2013.3-2015.2), M.Eng.; PhD from University of Aachen; currently Scientist at Bayer, Germany [https://www.linkedin.com/in/hyojin-kim-b3bb711ab Linkedin] (독일 바이엘 제약회사 선임 연구원)
**3. Hongseok Shim (2013.9-2015.8), M.Eng.; currently PhD student, Arizona State University, Biomedical Informatics program (애리조나주립대 생물정보학 박사과정)
**4. Sunmo Yang (2014.9-2017.2), M.Eng. currently Bioinformatics programmer, Yonsei University (연세대 네트워크생명공학 연구실 책임데이터연구원)
**5. Muyoung Lee (2016.3-2018.2), M.Eng. currently PhD student, University of Texas at Austin, Cellular and Molecular Biology Program (텍사스주립대 생물정보학 박사과정)
**6. Jiwon Yu (2021.9-2023.8), M.Eng. currently Data Scientist at [https://www.samsungbioepis.com/kr/index.do SAMSUNG BIOEPIS] (삼성바이오에피스 데이터사이언티스트)
**7. Geon_Koh (2022.9-2025.2), M.Eng. currently Researcher at Gachon University, College of Medicine (가천의대 시스템생물학 연구실 연구원)
**8. Wonjong Kim (2023.3-2025.8), M.Eng. currently Researcher at [https://samsungbiologics.com/ SAMSUNG Biologics] (삼성바이오로직스 연구원)

*'''Former Visiting Scientists/Students'''
**1. Minkyung Shin (2012.3-2012.7), went to University of Southern California graduate school
**2. Paul Chung (2012 summer), currently work at [https://about.meta.com/ Meta], USA
**3. Hyunjin Cho (2014 summer), currently Bioinformatics research assistant at [http://www.libd.org/ The Lieber Institute for Brain Development | LIBD], USA
**4. Michael Chung (2016.8-2016.12), currently work at [https://about.meta.com/ Meta], USA

*'''Former Undergraduate Students'''
**1. Ila Shin, went to medical school (Yonsei Univ.) Currently Professor, Kyunghee University School of Medicine (경희대학교 의과대학 교수)
**2. Yoonkyung Ko
**3. Sangyo Park, went to law school (Kyounghee Univ.)
**4. Jayoon Shin, went to medical school (Pusan National Univ.)
**5. Dongjoo Sun, went to dental school (Wongwang Univ.)
**6. Eulsoo Kim
**7. Myungwhan Lee, went to medical school (Yonsei Univ.)
**8. Moonhee Lee, went to graduate school (University of Amsterdam, Netherlands)
**9. Jinhyun Ju, went to graduate school (Cornell Medical School, Computational Systems Biology); Currently Principal Computational Biologist, Cancer Genomics at [https://bridgebio.com/ BridgeBio Pharma], Seattle, USA (미 바이오기업 선임연구원)
**10. Haeyoung Shin, went to graduate school (Brown University, Computational Neuroscience); Currently Professor, Seoul National University (서울대학교 생명과학부 교수)
**11. Joonghee Soh, went to graduate school (KAIST, Culture Technology)
**12. Hee Jung Cho, went to graduate school (UC Berkeley)
**13. TaeHwan Kim, went to medical school
**14. Joohyung Kim, went to medical school (Kyungpook National Univ.)
**15. Donghyun Shin, went to medical school (Yonsei Univ.)
**16. Byunghee Kang (2015 spring - 2016 summer), went to graduate school (PosTech)
**17. Sunphil Kim (2016 winter)
**18. Jaeho Shim (2016 winter)
**19. Seunghyun Shin (2016 spring)
**20. Aejoo Hong (2016 spring)
**21. Changbae Bang (2016 summer), went to medical school (Yonsei Univ.)
**22. Seoyoung Choi (2016 summer)
**23. Dabin Jung (2016 summer)
**24. Boreum Nam (2016 summer)
**25. Seungun Lee (2016 summer)
**26. Yeaji Kim (2016 summer and fall)
**27. Sangyoung Lee (2017 winter)
**28. Heejun Jang (2017 winter & spring), went to KIST as Research Assistant
**29. Jungha Lee (2017 summer), went to graduate school (Seoul National Univ.)
**30. Seunghyun Wang (2017 summer), went to graduate school (KAIST)
**31. Dong-Min Yang (2017 fall)
**32. Doo-Hee Lee (2017 fall)
**33. Suk-Jae Han (2018 winter)
**34. Ji-Eun Han (2018 winter)
**35. Yuri Ko (2018 spring)
**36. Sung-Woo Kim (2018 spring)
**37. Woosung Kwon (2018 summer)
**38. Soyun Kong (2018 summer)
**39. Hojeong Keum (2018 summer and fall)
**40. Sungjun Lim (2018 summer and fall)
**41. Jiyoon Lee (2018 summer and fall)
**42. Ilseok Choi(2019 winter, spring, summer and fall, 2020 winter, spring)
**43. Junik Park (2019 winter)
**44. Lee Yoo (2019 winter & spring)
**45. Yeonwha Kim (2019 winter & spring)
**46. Sohee Kim (2019 spring)
**47. Juseong Lee (2019 spring)
**48. Junyoung Yang (2019 spring & summer)
**49. Junyeong Ma (2019 summer, 2020 winter, summer, fall, 2021 winter)
**50. Dayeon Jung (2019 summer)
**51. Hanjoon Kim (2019 summer, 2021 winter)
**52. Hyungjin Kim (2020 winter, spring)
**53. Sujin Hyun (2020 winter)
**54. Hyuki Lee (2020 winter)
**55. Donghwan Lee (2020 winter)
**56. Jun Hyung Cha (2020 spring, summer)
**57. Jiwon Yu (2020 summer, 2021 Spring, summer)
**58. Dong Seok Kim (2020 summer)
**59. Donggeun Lee (2020 summer)
**60. Sehun Ahn (2020 summer, 2021 winter, spring, summer, 2022 winter)
**61. Jiho Kim (2020 summer)
**62. Euijung Seong (2020 fall, 2021 spring, summer)
**63. Junhan Kim (2021 winter & spring)
**64. Suyong Choi (2021 winter)
**65. Sujin Pyeon (2021 Spring)
**66. Hyeon Hee Ji (2021 Spring)
**67. Semin Kim (2021 Summer)
**68. Su Hwan Kim (2021 Summer)
**69. Yongbin Kim (2021 Summer)
**70. Nan Park (2021 Summer)
**71. Hoyong Jung (2021 Summer)
**72. Ingyeong Koh (2021 Summer)
**73. Jongbin Jeong (2022 Winter)
**74. Sungchul Yang (2022 Winter, Spring, Summer)
**75. Hyojung Lee (2022 Winter, Spring)
**76. Jun Hyeong Kim (2022 Winter, Spring)
**77. Young Ji Roh (2022 Spring, Summer)
**78. Geon Koh (2022 Spring, Summer)
**79. Hayoung Kang (2022 Summer, 2023 Spring)
**80. Won Jong Kim (2022 Summer, Fall, 2023 Winter)
**81. Christian Lee (2022 Summer)
**82. Je Yun Kang (2022 Summer)
**83. Sumin Lee (2022 Fall)
**84. Jungyeon Kim (2022 Fall, 2023 Winter)
**85. Seol Song (2023 Winter)
**86. Soyeon Kim (2023 Summer)
**87. Sieun Park (2023 Summer)
**88. Gunhyeong Lee (2023 Summer)
**89. Yunseo Han (2023 Summer)
**90. Jae Hyun Kim (2023 Summer)
**91. Jeong-min Seo (2023 Summer)
**92. Yerin Kim (2023 Fall, 2024 Winter)
**93. Sang Min Park (2024 Winter)
**94. Minsun Seo (2024 Winter)
**95. Jaeryun Sim (2024 Winter)
**96. Sun Min Lim (2024 Winter)
**97. Yurim Jung (2024 Spring, Summer)
**98. Hae Been Lee (2024 Spring, Summer)
**99. Zunu An (2024 Summer, Fall, 2025 Winter, Spring, Summer)
**100. Se Bin Lim (2024 Summer, Fall, 2025 Winter)
**101. Sang Min Yoon (2024 Summer)
**102. Yena Kim (2024 Summer)
**103. Kang Eon Lee (2024 Fall)
**104. Soyoon Park (2025 Winter)
**105. Sojung Lee (2025 Winter)
**106. Leanne Ma (2025 Winter)
**107. Seung Wan Jeon (2025 Summer)
**108. Joongun Lee (2025 Summer)
**109. Minseo Kim (2025 Summer)
**110. Hong Kyu Park (2025 Summer)
**111. Yunyeong Jang (2025 Fall, 2026 Winter)
**112. Jong Hyun Hwang (2025 Fall, 2026 Winter)
**113. Gyuweon Park (2025 Fall, 2026 Winter)

Media & Outreach

2025-11-15T00:01:19Z

Il1001:

{|border="0"
| width="100"|
*2025 Nov 14
|width="200" align="center"|
Clarivate BioWorld
|
[https://www.bioworld.com/articles/726031-most-complete-map-of-oral-microbiome-enables-links-to-systemic-disease?v=preview “Most complete’ map of oral microbiome enables links to systemic disease"]
|}
----
{|border="0"
| width="100"|
*2025 Oct 30
|width="200" align="center"|
동아사이언스
|
[https://www.dongascience.com/news.php?idx=74824 “장내 미생물 330종, 구강에도 있다…입속 미생물 지도 완성"]
|}
----
{|border="0"
| width="100"|
*2025 Oct 30
|width="200" align="center"|
매일경제
|
[https://www.mk.co.kr/news/it/11455826 “입안 미생물이 장 질환 일으킨다고? 세계 최대 구강 미생물 지도 완성"]
|}
----
{|border="0"
| width="100"|
*2025 Oct 30
|width="200" align="center"|
연세소식
|
[https://news.yonsei.ac.kr/kr/academia/detail?bbSeq=35355&bbCategory=fr “이인석 교수팀, 인체 구강 미생물의 ‘지도’ 완성"]
|}
----
{|border="0"
| width="100"|
*2025 Oct 30
|width="200" align="center"|
머니투데이
|
[https://www.mt.co.kr/thebio/2025/10/30/2025103009210927618 “두경부암 치료반응, 예측 길 열린다…'맞춤형 치료' 기대"]
|}
----
{|border="0"
| width="100"|
*2025 July 24
|width="200" align="center"|
머니투데이
|
[https://news.mt.co.kr/mtview.php?no=2025072409400232131 “입에서만 사는 세균, 대장암 세포에…환자 예후 나빴던 이유 찾았다"]
|}
----
{|border="0"
| width="100"|
*2025 July 24
|width="200" align="center"|
헤럴드경제
|
[https://biz.heraldcorp.com/article/10538639 “구강 세균 ‘푸조박테리아’, 대장암 예후 악화시켜…세브란스 연구팀 규명"]
|}
----
{|border="0"
| width="100"|
*2025 July 14
|width="200" align="center"|
연세대학교 생명시스템대학 소식지
|
[https://bio.yonsei.ac.kr/bio/board/trends.do?mode=view&articleNo=449517&article.offset=0&articleLimit=10 “이인석 교수, Golden Citation(최우수 피인용) 연구자 선정"]
|}
----
{|border="0"
| width="100"|
*2024 Dec 31
|width="200" align="center"|
동아일보
|
[https://www.donga.com/news/Health/article/all/20241230/130756741/2 “면역항암제 효과 높이는 핵심 단백질 발견"]
|}
----
{|border="0"
| width="100"|
*2024 Dec 30
|width="200" align="center"|
한국대학신문
|
[https://news.unn.net/news/articleView.html?idxno=573119 연세대, 면역항암제 효과 높이는 마이크로바이옴 유래 단백질 발견]
|}
----
{|border="0"
| width="100"|
*2024 Dec 16
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20241216171238142043&sr_site=S&sr_volume=636 언더우드 특훈교수 선정, 고원건‧김근수‧김현우‧박태영‧서지원‧염유식‧이인석 교수 세계적 수준의 연구 성과로 인류 발전에 기여]
|}
----
{|border="0"
| width="100"|
*2024 Sept 11
|width="200" align="center"|
뉴데일리경제
|
[https://biz.newdaily.co.kr/site/data/html/2024/09/11/2024091100135.html 연세대 이인석 교수팀, 장내 미생물 연구 정확도 높일 마우스 참조 유전체 40%이상 확장]
|}
----
{|border="0"
| width="100"|
*2024 June 27
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20240619104047616012&sr_volume=636 [연구 프론티어] 생명시스템대학·의료원 공동연구팀, 인유두종바이러스 양성 두경부암의 정밀 면역항암치료 타겟 제시]
|}
----
{|border="0"
| width="100"|
*2024 June 19
|width="200" align="center"|
중앙일보
|
[https://n.news.naver.com/article/025/0003367863?sid=103 연세대·세브란스 연구팀, 두경부암 면역항암치료 영향 요인 규명]
|}
----
{|border="0"
| width="100"|
*2024 Feb 16
|width="200" align="center"|
SBS News
|
[https://news.sbs.co.kr/news/endPage.do?news_id=N1007538975 미세플라스틱 섭취, 장 누수 유발 · 염증성 장질환 악화]
|}
----
{|border="0"
| width="100"|
*2024 Feb 16
|width="200" align="center"|
연합뉴스
|
[https://www.yna.co.kr/view/AKR20240216069000004 미세플라스틱 섭취, 장 누수 유발·염증성 장질환 악화]
|}
----
{|border="0"
| width="100"|
*2022 Dec 29
|width="200" align="center"|
조선일보
|
[http://news.chosun.com/pan/site/data/html_dir/2022/12/29/2022122900981.html 연세대 하상준·이인석 교수팀, 종양 미세환경 내 조절 T 세포의 안정성을 조절하는 PD-1의 역할 규명]
|}
----
{|border="0"
| width="100"|
*2022 Nov 21
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20221121093453881056&sr_site=S&sr_volume=632 [연구 프론티어] 이인석 교수팀, 세포 특이적 유전자 소셜 네트워크를 이용한 질병 연구법 개발]
|}
----
{|border="0"
| width="100"|
*2022 Nov 21
|width="200" align="center"|
교수신문
|
[http://www.kyosu.net/news/articleView.html?idxno=97075 연세대 이인석 교수팀, 세포 특이적 유전자 소셜 네트워크를 이용한 질병 연구법 개발]
|}
----
{|border="0"
| width="100"|
*2022 Nov 7
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20221107100002803079&sr_volume=632 [연구 프론티어] 이인석 교수팀, 난배양성 장내 미생물 유전체 해독 신기술 개발]
|}
----
{|border="0"
| width="100"|
*2022 Nov 1
|width="200" align="center"|
디지털타임스
|
[http://www.dt.co.kr/contents.html?article_no=2022110102109919608003&ref=naver 연세대 이인석 교수팀, 난배양성 장내 미생물 유전체 해독 신기술 개발]
|}
----
{|border="0"
| width="100"|
*2022 April 20
|width="200" align="center"|
연세소식
|
[http://www.yonsei.kr/ocx/news.jsp?mode=view&ar_seq=20220420144527941088&sr_site=S&sr_volume=631 2022 연세학술상에 김진우·이인석 교수]
|}
----
{|border="0"
| width="100"|
*2021 Oct 19
|width="200" align="center"|
헬스조선
|
[https://health.chosun.com/site/data/html_dir/2021/10/19/2021101901179.html 폐암 환자, 면역항암제 반응 예측 가능해져… 맞춤형 치료 가능성↑]
|}
----
{|border="0"
| width="100"|
*2021 Oct 19
|width="200" align="center"|
한국일보
|
[https://www.hankookilbo.com/News/Read/A2021101918070003750?did=NA 국내 암 사망률 1위’ 폐암, 면역 항암제 반응 예측 가능]
|}
----
{|border="0"
| width="100"|
*2021 Oct 19
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20211019095335963012&sr_volume=630&list_mode=list&sr_site=S&pager.offset=0&sr_cates=25 생명시스템대학·의과대학 연구팀, 단일세포 유전체 분석 기반 비소세포폐암 치료반응 예측 시그니처 발굴]
|}
----
{|border="0"
| width="100"|
*2021 Sep 7
|width="200" align="center"|
연세소식영문판
|
[https://www.yonsei.ac.kr/en_sc/research/archive-view.jsp?article_no=198925&board_wrapper=%2Fen_sc%2Fresearch%2Farchive.jsp&pager.offset=0&board_no=584&title=decoding-the-human-microbiomes:-creating-a-comprehensive-map-of-human-intestinal-flora Decoding the human microbiomes: creating a comprehensive map of human intestinal flora]
|}
----
{|border="0"
| width="100"|
*2021 Aug 27
|width="200" align="center"|
조선일보
|
[https://lifenlearning.chosun.com/pan/site/data/html_dir/2021/08/27/2021082700724.html 연세대 이인석 교수팀, 인간 표준 장내 마이크로바이옴 유전체 지도 구축]
|}
----
{|border="0"
| width="100"|
*2021 Aug 27
|width="200" align="center"|
중앙일보
|
[https://www.joongang.co.kr/article/25002045#home 연세대 이인석 교수팀, 인간 표준 장내 마이크로바이옴 유전체 지도 구축]
|}
----
{|border="0"
| width="100"|
*2021 Aug 27
|width="200" align="center"|
동아사이언스
|
[https://m.dongascience.com/news.php?idx=48981 한국인 장내미생물 유전자 지도 처음 나왔다]
|}
----
{|border="0"
| width="100"|
*2021 Aug 27
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20210827093744195080&sr_site=S&sr_volume=630 이인석 교수팀, 인간 표준 장내 마이크로바이옴 유전체 지도 구축]
|}
----
{|border="0"
| width="100"|
*2020 Mar 31
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20200331164058624094&sr_volume=626&list_mode=list&sr_site=S&pager.offset=0&sr_cates=25 이인석, 하상준 교수 공동 연구팀, 면역항암치료 효능 개선의 새로운 가능성 제시]
|}
----
{|border="0"
| width="100"|
*2020 Mar 16
|width="200" align="center"|
헤럴드경제
|
[http://news.heraldcorp.com/view.php?ud=20200313000812 면역세포 기능 회복으로 암세포 사멸 유도한다]
|}
----
{|border="0"
| width="100"|
*2020 Mar 16
|width="200" align="center"|
파이낸셜뉴스
|
[https://www.fnnews.com/news/202003151159173040 면역항암치료제 효능이 떨어지는 원인 찾았다]
|}
----
{|border="0"
| width="100"|
*2018 Dec 04
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20181204123907677066&sr_volume=619&list_mode=list&sr_site=S&pager.offset=0&sr_cates=25 이인석 교수 연구팀, 시스템의학을 위한 휴먼유전자네트워크 개발]
|}
----
{|border="0"
| width="100"|
*2017 Dec 05
|width="200" align="center"|
연세소식
|
[http://www.yonsei.ac.kr/ocx/news.jsp?mode=view&sr_site=S&ar_seq=20171203015403938027&&sr_volume=613 이인석 교수 연구팀, 과학기술 문헌 빅데이터 분석을 통한 세계 최대 유전자조절 네트워크 개발]
|}
----
{|border="0"
| width="100"|
*2017 June 01
|width="200" align="center"|
연세소식
|
[[media:GWAB_yonsei.pdf|이인석 교수 연구팀, 유전체코호트 네트워크 분석을 통한 질병 유전자 예측 시스템 개발]]
|}
----
{|border="0"
| width="100"|
*2016 Dec 06
|width="200" align="center"|
연세소식
|
[http://www.yonsei.ac.kr/ocx/news.jsp?mode=view&sr_site=S&ar_seq=20161205075723950030&&sr_volume=603 이인석 교수 연구팀, 빅데이터 기반 질환유전자 예측시스템 개발]
|}
----
{|border="0"
| width="100"|
*2016 Nov 14
|width="200" align="center"|
연세춘추
|
[[media:20161114-연세춘추-이인석.pdf|암유전자의 소셜네트워크를 보다]]
|}
----
{|border="0"
| width="100"|
*2016 Sep 2
|width="200" align="center"|
연세소식
|
[[media:201609-연세소식-이인석.pdf|이인석 교수팀, 유전자 소셜 네트워크로 암유전자 찾아낸다]]
|}
----
{|border="0"
| width="100"|
*2016 June 27
|width="200" align="center"|
연합뉴스
|
[http://www.yonhapnews.co.kr/bulletin/2016/06/25/0200000000AKR20160625014300017.HTML?input=1195m 네트워크' 이용해 암 유전자 찾는 새 시스템 개발]
|}
----
{|border="0"
| width="100"|
*2016 June 27
|width="200" align="center"|
매일경제
|
[http://news.mk.co.kr/newsRead.php?no=457258&year=2016 유전자 소셜 네트워크로 癌유발 유전자 찾는다]
|}
----
{|border="0"
| width="100"|
*2016 June 27
|width="200" align="center"|
동아일보
|
[http://news.donga.com/3/all/20160626/78865398/1 국내 연구진, 희귀암 등 새로운 암 유발 유전자 찾는 시스템 개발]
|}
----
{|border="0"
| width="100"|
*2016 June 27
|width="200" align="center"|
YTN Science
|
[http://science.ytn.co.kr/program/program_view.php?s_mcd=0082&s_hcd=&key=201606271111574798 유전자 지도로 암 유발 유전자 예측]
|}
----
{|border="0"
| width="100"|
*2016 Feb 4
|width="200" align="center"|
연세소식
|
[[media:역분화인자발굴.pdf|이인석 교수 연구팀, 시스템생물학 기반 줄기세포 역분화 효율 증진인자 발굴]]
|}
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{|border="0"
| width="100"|
*2015 Dec 7
|width="200" align="center"|
연세소식
|
[[media:연세소식기사_MouseNet.pdf|이인석 교수 연구팀, 세계 최대 규모 실험용 흰쥐 유전자 네트워크 MouseNet 개발]]
|}
----
{|border="0"
| width="100"|
*2015 April 16
|width="200" align="center"|
연세소식
|
[[media:Yonseisosik.pdf|이인석 교수 연구팀, 빅데이터 기반 유전자네트워크를 이용한 작물연구 관련 종설과 연구논문 발표]]
|}
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{|border="0"
| width="100"|
*2014 Oct 30
|width="200" align="center"|
Yonsei Research Magazine
|
[[media:Yonsei_Research_Magazine.pdf|Professor Lee Insuk's Research Team Finds a New Way to Study Human Diseases]]
|}
----
{|border="0"
| width="100"|
*2014 July 16
|width="200" align="center"|
ScienceTimes
|
[http://www.sciencetimes.co.kr/?news=%EC%A7%88%EB%B3%91-%EC%B9%98%EB%A3%8C-%EC%A0%95%ED%99%95%ED%95%9C-%EC%9B%90%EC%9D%B8%EC%A7%84%EB%8B%A8%EC%9D%B4-%EB%A8%BC%EC%A0%80%EC%A3%A0 “질병 치료, 정확한 원인진단이 먼저죠”]
|}
----
{|border="0"
| width="100"|
*2014 June 25
|width="200" align="center"|
한국경제
|
[[media:morphin_article.jpg|유전자-질환 연관성 예측시스템 나왔다]]
|}
----
{|border="0"
| width="100"|
*2014 June 24
|width="200" align="center"|
YTN Science
|
[https://www.youtube.com/watch?v=tpiGS5cArY4 유전자 상관관계 네트워크로 질환 연구]
|}
----
{|border="0"
| width="100"|
*2012 Nov 22
|width="200" align="center"|
5th RECOMB Conference on Regulatory and Systems Genomics
|
[http://recomb-2012.c2b2.columbia.edu/?q=node/29 HumanNet 논문(Genome Research 21:1109)이 2011년 시스템생물학 분야에서 가장 영향력 있는 논문 탑10에 선정]
|}
----
{|border="0"
| width="100"|
*2011 Nov 9
|width="200" align="center"|
YTN Science 24
|
[http://www.sciencetv.kr/program/program_view.php?s_mcd=0184&s_hcd=01&key=201111091542149116 벼 유전자 네트워크 완성...슈퍼 벼 생산]
|}
----
{|border="0"
| width="100"|
*2011 Nov 1
|width="200" align="center"|
KBS News
|
[http://news.kbs.co.kr/science/2011/11/01/2381579.html 병충해·홍수에 강한 ‘슈퍼 벼’ 개발]

보도내용 중 이화여대연구진을 연세대학교 연구진 으로 정정합니다
|}
----
{|border="0"
| width="100"|
*2011 Nov 1
|width="200" align="center"|
Dong-A Ilbo Channel A News
|
[http://news.donga.com/3/all/20111104/41645483/1 벼 유전자 네트워크]
|}
----
{|border="0"
| width="100"|
*2011 Oct 3
|width="200" align="center"|
The financial news
|
[[media:Media_n_Outreach_019.pdf|한국 과학의 미래，이젠 노벨상이다(2): ④ 미로처럼 얽힌 유전자 네트워크 지도화]]

|}
----

{|border="0"
| width="100"|
*2011 Aug 31
|width="200" align="center"|
MBN News
|
[http://tvnews.media.daum.net/view.html?cateid=100000&newsid=20110831141310630&p=mbn[수요일에 만난 과학자] 유전자의 소셜 네트워크를 밝힌다
]

|}
----

{|border="0"
| width="100"|
*2011 May
|width="200" align="center"|
KBS News
|
[http://news.kbs.co.kr/science/2011/05/12/2290284.html '휴먼 넷' 난치성 질환 치료 해법 찾아]

|}
----

{|border="0"
| width="100"|
*2011 May
|width="200" align="center"|
News Letter Yonsei
|
[[media:Media_n_Outreach_018.pdf|유전자 소셜 네트워크로 암, 당뇨 조절 유전자 발굴법 개발]]

|}
----
{|border="0"
| rowspan = "2" width="100"|
*2011 May
|width="200" align="center"|
Digital times
|
[[media:Media_n_Outreach_017.pdf|유전자 네트워크로 질병 규명]]
|-
|width="200" align="center"|
The Kyunghyang Daily News
|
[[media:Media_n_Outreach_017.pdf|유전자와 유전자의 '관계' 네트워크 지도 개발]]
|}
----
{|border="0"
| width="100"|
*2011 Feb
|width="200" align="center"|
The Chosunilbo
|
[[media:Media_n_Outreach_016.pdf|인간 세상 네트워크 닮은 식물 유전자의 세계]]

|}
----
{|border="0"
| width="100"|
*2011 Feb
|width="200" align="center"|
Science : Visualization Challenge
|
[[media:Media_n_Outreach_015.pdf|AraNet: A Genome-wide Gene Function Association Network for ''Arabidopsis thaliana'']]

|}
----
{|border="0"
| width="100"|
*2010 Nov
|width="200" align="center"|
POSCO News
|
[[media:Media_n_Outreach_014.pdf|'2011청암펠로우(이인석 교수 선정)]]

|}
----
{|border="0"
| width="100"|
*2010 Sep
|width="200" align="center"|
News Letter Yonsei
|
[[media:Media_n_Outreach_013.pdf|생명공학과 학부생 연구결과 국제 권위 저널에 실려 (김이루 학생)]]

|}
----
{|border="0"
| width="100"|
*2010 Aug
|width="200" align="center"|
The Chosunilbo
|
[[media:Media_n_Outreach_012.pdf|연세대 학부생 생명공학 논문 국제학술지 게재 (김이루 학생)]]

|}
----
{|border="0"
| width="100"|
*2010 Aug
|width="200" align="center"|
The Science & technology
|
[[media:Media_n_Outreach_011.pdf|유전자네트워크 이용한 복잡질환 조절유전자 예측방법 개발 (논단)]]

|}
----
{|border="0"
| width="100"|
*2010 Jul
|width="200" align="center"|
News Letter Yonsei
|
[[media:Media_n_Outreach_010.pdf|이인석 교수, 암,당뇨 등의 새로운 치료법 가능성 열어]]

|}
----
{|border="0"
| rowspan = "2" width="100"|
*2010 Jun
|width="200" align="center"|
Kukminilbo
|
[[media:Media_n_Outreach_009.pdf|암,당뇨병 등 복잡 질환 조절 유전자 효율적으로 찾아내는 새로운 방법 개발]]
|-
|width="200" align="center"|
Seoul newspaper
|
[[media:Media_n_Outreach_009.pdf|암,당뇨 등 '조절 유전자 예측법' 개발]]
|}
----
{|border="0"
| width="100"|
*2010 Mar
|width="200" align="center"|
The Yonsei Chunchu (Daily newspaper of Yonsei University)
|
[[media:Media_n_Outreach_008.pdf|'예측'이 가장 쉬웠어요]]

|}
----
{|border="0"
| width="100"|
*2010 Mar
|width="200" align="center"|
News Letter Yonsei
|
[[media:Media_n_Outreach_007.pdf|이인석교수, 세계 최대 식물유전자네트워크 규명]]

|}
----
{|border="0"
| width="100"|
*2010 Mar
|width="200" align="center"|
The Science & technology
|
[[media:Media_n_Outreach_006.pdf|네트워크 이용한 새롭고 효율적인 유전학 연구 기법 제시 (논단)]]

|}
----
{|border="0"
| width="100"|
*2010 Mar
|width="200" align="center"|
Biomedical Computation Review (IT magazine)
|
[[media:Media_n_Outreach_005.pdf|A Tipping Point for Function Prediction]]

|}
----
{|border="0"
| width="100"|
*2010 Feb
|width="200" align="center"|
The Korea Economic Daily
|
[[media:Media_n_Outreach_004.pdf|식물도 사람처럼 유전자 네트워크가 있었네!]]

|}
----
{|border="0" width="730"
| width="100"|
*2010 Feb
|width="200" align="center"|
The Chosunilbo
|
[[media:Media_n_Outreach_003.pdf|유전자 숨겨진 기능 쉽게 찾는 '네트워크 기술']]

|}
----
{|border="0"
| width="100"|
*2010 Feb
|width="200" align="center"|
Science Daily
|
[[media:Media_n_Outreach_002.pdf|Gene Function Discovery: New Computation Model Predicts Gene Function]]

|}
----
{|border="0"
|width="100"|
*2008 Dec
|width="200" align="center"|
KSMCB (Korean Society for Molecular and Cellular Biology) news
|
[[media:Media_n_Outreach_001.pdf|기능성유전자 네트워크를 이용한 생물학 연구 (논단)]]

|}
----

Media & Outreach

2025-11-15T00:00:51Z

Il1001:

{|border="0"
| width="100"|
*2025 Oct 30
|width="200" align="center"|
Clarivate BioWorld
|
[https://www.bioworld.com/articles/726031-most-complete-map-of-oral-microbiome-enables-links-to-systemic-disease?v=preview “Most complete’ map of oral microbiome enables links to systemic disease"]
|}
----
{|border="0"
| width="100"|
*2025 Oct 30
|width="200" align="center"|
동아사이언스
|
[https://www.dongascience.com/news.php?idx=74824 “장내 미생물 330종, 구강에도 있다…입속 미생물 지도 완성"]
|}
----
{|border="0"
| width="100"|
*2025 Oct 30
|width="200" align="center"|
매일경제
|
[https://www.mk.co.kr/news/it/11455826 “입안 미생물이 장 질환 일으킨다고? 세계 최대 구강 미생물 지도 완성"]
|}
----
{|border="0"
| width="100"|
*2025 Oct 30
|width="200" align="center"|
연세소식
|
[https://news.yonsei.ac.kr/kr/academia/detail?bbSeq=35355&bbCategory=fr “이인석 교수팀, 인체 구강 미생물의 ‘지도’ 완성"]
|}
----
{|border="0"
| width="100"|
*2025 Oct 30
|width="200" align="center"|
머니투데이
|
[https://www.mt.co.kr/thebio/2025/10/30/2025103009210927618 “두경부암 치료반응, 예측 길 열린다…'맞춤형 치료' 기대"]
|}
----
{|border="0"
| width="100"|
*2025 July 24
|width="200" align="center"|
머니투데이
|
[https://news.mt.co.kr/mtview.php?no=2025072409400232131 “입에서만 사는 세균, 대장암 세포에…환자 예후 나빴던 이유 찾았다"]
|}
----
{|border="0"
| width="100"|
*2025 July 24
|width="200" align="center"|
헤럴드경제
|
[https://biz.heraldcorp.com/article/10538639 “구강 세균 ‘푸조박테리아’, 대장암 예후 악화시켜…세브란스 연구팀 규명"]
|}
----
{|border="0"
| width="100"|
*2025 July 14
|width="200" align="center"|
연세대학교 생명시스템대학 소식지
|
[https://bio.yonsei.ac.kr/bio/board/trends.do?mode=view&articleNo=449517&article.offset=0&articleLimit=10 “이인석 교수, Golden Citation(최우수 피인용) 연구자 선정"]
|}
----
{|border="0"
| width="100"|
*2024 Dec 31
|width="200" align="center"|
동아일보
|
[https://www.donga.com/news/Health/article/all/20241230/130756741/2 “면역항암제 효과 높이는 핵심 단백질 발견"]
|}
----
{|border="0"
| width="100"|
*2024 Dec 30
|width="200" align="center"|
한국대학신문
|
[https://news.unn.net/news/articleView.html?idxno=573119 연세대, 면역항암제 효과 높이는 마이크로바이옴 유래 단백질 발견]
|}
----
{|border="0"
| width="100"|
*2024 Dec 16
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20241216171238142043&sr_site=S&sr_volume=636 언더우드 특훈교수 선정, 고원건‧김근수‧김현우‧박태영‧서지원‧염유식‧이인석 교수 세계적 수준의 연구 성과로 인류 발전에 기여]
|}
----
{|border="0"
| width="100"|
*2024 Sept 11
|width="200" align="center"|
뉴데일리경제
|
[https://biz.newdaily.co.kr/site/data/html/2024/09/11/2024091100135.html 연세대 이인석 교수팀, 장내 미생물 연구 정확도 높일 마우스 참조 유전체 40%이상 확장]
|}
----
{|border="0"
| width="100"|
*2024 June 27
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20240619104047616012&sr_volume=636 [연구 프론티어] 생명시스템대학·의료원 공동연구팀, 인유두종바이러스 양성 두경부암의 정밀 면역항암치료 타겟 제시]
|}
----
{|border="0"
| width="100"|
*2024 June 19
|width="200" align="center"|
중앙일보
|
[https://n.news.naver.com/article/025/0003367863?sid=103 연세대·세브란스 연구팀, 두경부암 면역항암치료 영향 요인 규명]
|}
----
{|border="0"
| width="100"|
*2024 Feb 16
|width="200" align="center"|
SBS News
|
[https://news.sbs.co.kr/news/endPage.do?news_id=N1007538975 미세플라스틱 섭취, 장 누수 유발 · 염증성 장질환 악화]
|}
----
{|border="0"
| width="100"|
*2024 Feb 16
|width="200" align="center"|
연합뉴스
|
[https://www.yna.co.kr/view/AKR20240216069000004 미세플라스틱 섭취, 장 누수 유발·염증성 장질환 악화]
|}
----
{|border="0"
| width="100"|
*2022 Dec 29
|width="200" align="center"|
조선일보
|
[http://news.chosun.com/pan/site/data/html_dir/2022/12/29/2022122900981.html 연세대 하상준·이인석 교수팀, 종양 미세환경 내 조절 T 세포의 안정성을 조절하는 PD-1의 역할 규명]
|}
----
{|border="0"
| width="100"|
*2022 Nov 21
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20221121093453881056&sr_site=S&sr_volume=632 [연구 프론티어] 이인석 교수팀, 세포 특이적 유전자 소셜 네트워크를 이용한 질병 연구법 개발]
|}
----
{|border="0"
| width="100"|
*2022 Nov 21
|width="200" align="center"|
교수신문
|
[http://www.kyosu.net/news/articleView.html?idxno=97075 연세대 이인석 교수팀, 세포 특이적 유전자 소셜 네트워크를 이용한 질병 연구법 개발]
|}
----
{|border="0"
| width="100"|
*2022 Nov 7
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20221107100002803079&sr_volume=632 [연구 프론티어] 이인석 교수팀, 난배양성 장내 미생물 유전체 해독 신기술 개발]
|}
----
{|border="0"
| width="100"|
*2022 Nov 1
|width="200" align="center"|
디지털타임스
|
[http://www.dt.co.kr/contents.html?article_no=2022110102109919608003&ref=naver 연세대 이인석 교수팀, 난배양성 장내 미생물 유전체 해독 신기술 개발]
|}
----
{|border="0"
| width="100"|
*2022 April 20
|width="200" align="center"|
연세소식
|
[http://www.yonsei.kr/ocx/news.jsp?mode=view&ar_seq=20220420144527941088&sr_site=S&sr_volume=631 2022 연세학술상에 김진우·이인석 교수]
|}
----
{|border="0"
| width="100"|
*2021 Oct 19
|width="200" align="center"|
헬스조선
|
[https://health.chosun.com/site/data/html_dir/2021/10/19/2021101901179.html 폐암 환자, 면역항암제 반응 예측 가능해져… 맞춤형 치료 가능성↑]
|}
----
{|border="0"
| width="100"|
*2021 Oct 19
|width="200" align="center"|
한국일보
|
[https://www.hankookilbo.com/News/Read/A2021101918070003750?did=NA 국내 암 사망률 1위’ 폐암, 면역 항암제 반응 예측 가능]
|}
----
{|border="0"
| width="100"|
*2021 Oct 19
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20211019095335963012&sr_volume=630&list_mode=list&sr_site=S&pager.offset=0&sr_cates=25 생명시스템대학·의과대학 연구팀, 단일세포 유전체 분석 기반 비소세포폐암 치료반응 예측 시그니처 발굴]
|}
----
{|border="0"
| width="100"|
*2021 Sep 7
|width="200" align="center"|
연세소식영문판
|
[https://www.yonsei.ac.kr/en_sc/research/archive-view.jsp?article_no=198925&board_wrapper=%2Fen_sc%2Fresearch%2Farchive.jsp&pager.offset=0&board_no=584&title=decoding-the-human-microbiomes:-creating-a-comprehensive-map-of-human-intestinal-flora Decoding the human microbiomes: creating a comprehensive map of human intestinal flora]
|}
----
{|border="0"
| width="100"|
*2021 Aug 27
|width="200" align="center"|
조선일보
|
[https://lifenlearning.chosun.com/pan/site/data/html_dir/2021/08/27/2021082700724.html 연세대 이인석 교수팀, 인간 표준 장내 마이크로바이옴 유전체 지도 구축]
|}
----
{|border="0"
| width="100"|
*2021 Aug 27
|width="200" align="center"|
중앙일보
|
[https://www.joongang.co.kr/article/25002045#home 연세대 이인석 교수팀, 인간 표준 장내 마이크로바이옴 유전체 지도 구축]
|}
----
{|border="0"
| width="100"|
*2021 Aug 27
|width="200" align="center"|
동아사이언스
|
[https://m.dongascience.com/news.php?idx=48981 한국인 장내미생물 유전자 지도 처음 나왔다]
|}
----
{|border="0"
| width="100"|
*2021 Aug 27
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20210827093744195080&sr_site=S&sr_volume=630 이인석 교수팀, 인간 표준 장내 마이크로바이옴 유전체 지도 구축]
|}
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{|border="0"
| width="100"|
*2020 Mar 31
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20200331164058624094&sr_volume=626&list_mode=list&sr_site=S&pager.offset=0&sr_cates=25 이인석, 하상준 교수 공동 연구팀, 면역항암치료 효능 개선의 새로운 가능성 제시]
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{|border="0"
| width="100"|
*2020 Mar 16
|width="200" align="center"|
헤럴드경제
|
[http://news.heraldcorp.com/view.php?ud=20200313000812 면역세포 기능 회복으로 암세포 사멸 유도한다]
|}
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{|border="0"
| width="100"|
*2020 Mar 16
|width="200" align="center"|
파이낸셜뉴스
|
[https://www.fnnews.com/news/202003151159173040 면역항암치료제 효능이 떨어지는 원인 찾았다]
|}
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{|border="0"
| width="100"|
*2018 Dec 04
|width="200" align="center"|
연세소식
|
[https://www.yonsei.ac.kr/ocx/news.jsp?mode=view&ar_seq=20181204123907677066&sr_volume=619&list_mode=list&sr_site=S&pager.offset=0&sr_cates=25 이인석 교수 연구팀, 시스템의학을 위한 휴먼유전자네트워크 개발]
|}
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{|border="0"
| width="100"|
*2017 Dec 05
|width="200" align="center"|
연세소식
|
[http://www.yonsei.ac.kr/ocx/news.jsp?mode=view&sr_site=S&ar_seq=20171203015403938027&&sr_volume=613 이인석 교수 연구팀, 과학기술 문헌 빅데이터 분석을 통한 세계 최대 유전자조절 네트워크 개발]
|}
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{|border="0"
| width="100"|
*2017 June 01
|width="200" align="center"|
연세소식
|
[[media:GWAB_yonsei.pdf|이인석 교수 연구팀, 유전체코호트 네트워크 분석을 통한 질병 유전자 예측 시스템 개발]]
|}
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{|border="0"
| width="100"|
*2016 Dec 06
|width="200" align="center"|
연세소식
|
[http://www.yonsei.ac.kr/ocx/news.jsp?mode=view&sr_site=S&ar_seq=20161205075723950030&&sr_volume=603 이인석 교수 연구팀, 빅데이터 기반 질환유전자 예측시스템 개발]
|}
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{|border="0"
| width="100"|
*2016 Nov 14
|width="200" align="center"|
연세춘추
|
[[media:20161114-연세춘추-이인석.pdf|암유전자의 소셜네트워크를 보다]]
|}
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{|border="0"
| width="100"|
*2016 Sep 2
|width="200" align="center"|
연세소식
|
[[media:201609-연세소식-이인석.pdf|이인석 교수팀, 유전자 소셜 네트워크로 암유전자 찾아낸다]]
|}
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{|border="0"
| width="100"|
*2016 June 27
|width="200" align="center"|
연합뉴스
|
[http://www.yonhapnews.co.kr/bulletin/2016/06/25/0200000000AKR20160625014300017.HTML?input=1195m 네트워크' 이용해 암 유전자 찾는 새 시스템 개발]
|}
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{|border="0"
| width="100"|
*2016 June 27
|width="200" align="center"|
매일경제
|
[http://news.mk.co.kr/newsRead.php?no=457258&year=2016 유전자 소셜 네트워크로 癌유발 유전자 찾는다]
|}
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{|border="0"
| width="100"|
*2016 June 27
|width="200" align="center"|
동아일보
|
[http://news.donga.com/3/all/20160626/78865398/1 국내 연구진, 희귀암 등 새로운 암 유발 유전자 찾는 시스템 개발]
|}
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{|border="0"
| width="100"|
*2016 June 27
|width="200" align="center"|
YTN Science
|
[http://science.ytn.co.kr/program/program_view.php?s_mcd=0082&s_hcd=&key=201606271111574798 유전자 지도로 암 유발 유전자 예측]
|}
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{|border="0"
| width="100"|
*2016 Feb 4
|width="200" align="center"|
연세소식
|
[[media:역분화인자발굴.pdf|이인석 교수 연구팀, 시스템생물학 기반 줄기세포 역분화 효율 증진인자 발굴]]
|}
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{|border="0"
| width="100"|
*2015 Dec 7
|width="200" align="center"|
연세소식
|
[[media:연세소식기사_MouseNet.pdf|이인석 교수 연구팀, 세계 최대 규모 실험용 흰쥐 유전자 네트워크 MouseNet 개발]]
|}
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{|border="0"
| width="100"|
*2015 April 16
|width="200" align="center"|
연세소식
|
[[media:Yonseisosik.pdf|이인석 교수 연구팀, 빅데이터 기반 유전자네트워크를 이용한 작물연구 관련 종설과 연구논문 발표]]
|}
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{|border="0"
| width="100"|
*2014 Oct 30
|width="200" align="center"|
Yonsei Research Magazine
|
[[media:Yonsei_Research_Magazine.pdf|Professor Lee Insuk's Research Team Finds a New Way to Study Human Diseases]]
|}
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{|border="0"
| width="100"|
*2014 July 16
|width="200" align="center"|
ScienceTimes
|
[http://www.sciencetimes.co.kr/?news=%EC%A7%88%EB%B3%91-%EC%B9%98%EB%A3%8C-%EC%A0%95%ED%99%95%ED%95%9C-%EC%9B%90%EC%9D%B8%EC%A7%84%EB%8B%A8%EC%9D%B4-%EB%A8%BC%EC%A0%80%EC%A3%A0 “질병 치료, 정확한 원인진단이 먼저죠”]
|}
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{|border="0"
| width="100"|
*2014 June 25
|width="200" align="center"|
한국경제
|
[[media:morphin_article.jpg|유전자-질환 연관성 예측시스템 나왔다]]
|}
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{|border="0"
| width="100"|
*2014 June 24
|width="200" align="center"|
YTN Science
|
[https://www.youtube.com/watch?v=tpiGS5cArY4 유전자 상관관계 네트워크로 질환 연구]
|}
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{|border="0"
| width="100"|
*2012 Nov 22
|width="200" align="center"|
5th RECOMB Conference on Regulatory and Systems Genomics
|
[http://recomb-2012.c2b2.columbia.edu/?q=node/29 HumanNet 논문(Genome Research 21:1109)이 2011년 시스템생물학 분야에서 가장 영향력 있는 논문 탑10에 선정]
|}
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{|border="0"
| width="100"|
*2011 Nov 9
|width="200" align="center"|
YTN Science 24
|
[http://www.sciencetv.kr/program/program_view.php?s_mcd=0184&s_hcd=01&key=201111091542149116 벼 유전자 네트워크 완성...슈퍼 벼 생산]
|}
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{|border="0"
| width="100"|
*2011 Nov 1
|width="200" align="center"|
KBS News
|
[http://news.kbs.co.kr/science/2011/11/01/2381579.html 병충해·홍수에 강한 ‘슈퍼 벼’ 개발]

보도내용 중 이화여대연구진을 연세대학교 연구진 으로 정정합니다
|}
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{|border="0"
| width="100"|
*2011 Nov 1
|width="200" align="center"|
Dong-A Ilbo Channel A News
|
[http://news.donga.com/3/all/20111104/41645483/1 벼 유전자 네트워크]
|}
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{|border="0"
| width="100"|
*2011 Oct 3
|width="200" align="center"|
The financial news
|
[[media:Media_n_Outreach_019.pdf|한국 과학의 미래，이젠 노벨상이다(2): ④ 미로처럼 얽힌 유전자 네트워크 지도화]]

|}
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{|border="0"
| width="100"|
*2011 Aug 31
|width="200" align="center"|
MBN News
|
[http://tvnews.media.daum.net/view.html?cateid=100000&newsid=20110831141310630&p=mbn[수요일에 만난 과학자] 유전자의 소셜 네트워크를 밝힌다
]

|}
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{|border="0"
| width="100"|
*2011 May
|width="200" align="center"|
KBS News
|
[http://news.kbs.co.kr/science/2011/05/12/2290284.html '휴먼 넷' 난치성 질환 치료 해법 찾아]

|}
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{|border="0"
| width="100"|
*2011 May
|width="200" align="center"|
News Letter Yonsei
|
[[media:Media_n_Outreach_018.pdf|유전자 소셜 네트워크로 암, 당뇨 조절 유전자 발굴법 개발]]

|}
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{|border="0"
| rowspan = "2" width="100"|
*2011 May
|width="200" align="center"|
Digital times
|
[[media:Media_n_Outreach_017.pdf|유전자 네트워크로 질병 규명]]
|-
|width="200" align="center"|
The Kyunghyang Daily News
|
[[media:Media_n_Outreach_017.pdf|유전자와 유전자의 '관계' 네트워크 지도 개발]]
|}
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{|border="0"
| width="100"|
*2011 Feb
|width="200" align="center"|
The Chosunilbo
|
[[media:Media_n_Outreach_016.pdf|인간 세상 네트워크 닮은 식물 유전자의 세계]]

|}
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{|border="0"
| width="100"|
*2011 Feb
|width="200" align="center"|
Science : Visualization Challenge
|
[[media:Media_n_Outreach_015.pdf|AraNet: A Genome-wide Gene Function Association Network for ''Arabidopsis thaliana'']]

|}
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{|border="0"
| width="100"|
*2010 Nov
|width="200" align="center"|
POSCO News
|
[[media:Media_n_Outreach_014.pdf|'2011청암펠로우(이인석 교수 선정)]]

|}
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{|border="0"
| width="100"|
*2010 Sep
|width="200" align="center"|
News Letter Yonsei
|
[[media:Media_n_Outreach_013.pdf|생명공학과 학부생 연구결과 국제 권위 저널에 실려 (김이루 학생)]]

|}
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{|border="0"
| width="100"|
*2010 Aug
|width="200" align="center"|
The Chosunilbo
|
[[media:Media_n_Outreach_012.pdf|연세대 학부생 생명공학 논문 국제학술지 게재 (김이루 학생)]]

|}
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{|border="0"
| width="100"|
*2010 Aug
|width="200" align="center"|
The Science & technology
|
[[media:Media_n_Outreach_011.pdf|유전자네트워크 이용한 복잡질환 조절유전자 예측방법 개발 (논단)]]

|}
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{|border="0"
| width="100"|
*2010 Jul
|width="200" align="center"|
News Letter Yonsei
|
[[media:Media_n_Outreach_010.pdf|이인석 교수, 암,당뇨 등의 새로운 치료법 가능성 열어]]

|}
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{|border="0"
| rowspan = "2" width="100"|
*2010 Jun
|width="200" align="center"|
Kukminilbo
|
[[media:Media_n_Outreach_009.pdf|암,당뇨병 등 복잡 질환 조절 유전자 효율적으로 찾아내는 새로운 방법 개발]]
|-
|width="200" align="center"|
Seoul newspaper
|
[[media:Media_n_Outreach_009.pdf|암,당뇨 등 '조절 유전자 예측법' 개발]]
|}
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{|border="0"
| width="100"|
*2010 Mar
|width="200" align="center"|
The Yonsei Chunchu (Daily newspaper of Yonsei University)
|
[[media:Media_n_Outreach_008.pdf|'예측'이 가장 쉬웠어요]]

|}
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{|border="0"
| width="100"|
*2010 Mar
|width="200" align="center"|
News Letter Yonsei
|
[[media:Media_n_Outreach_007.pdf|이인석교수, 세계 최대 식물유전자네트워크 규명]]

|}
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{|border="0"
| width="100"|
*2010 Mar
|width="200" align="center"|
The Science & technology
|
[[media:Media_n_Outreach_006.pdf|네트워크 이용한 새롭고 효율적인 유전학 연구 기법 제시 (논단)]]

|}
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{|border="0"
| width="100"|
*2010 Mar
|width="200" align="center"|
Biomedical Computation Review (IT magazine)
|
[[media:Media_n_Outreach_005.pdf|A Tipping Point for Function Prediction]]

|}
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{|border="0"
| width="100"|
*2010 Feb
|width="200" align="center"|
The Korea Economic Daily
|
[[media:Media_n_Outreach_004.pdf|식물도 사람처럼 유전자 네트워크가 있었네!]]

|}
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{|border="0" width="730"
| width="100"|
*2010 Feb
|width="200" align="center"|
The Chosunilbo
|
[[media:Media_n_Outreach_003.pdf|유전자 숨겨진 기능 쉽게 찾는 '네트워크 기술']]

|}
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{|border="0"
| width="100"|
*2010 Feb
|width="200" align="center"|
Science Daily
|
[[media:Media_n_Outreach_002.pdf|Gene Function Discovery: New Computation Model Predicts Gene Function]]

|}
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{|border="0"
|width="100"|
*2008 Dec
|width="200" align="center"|
KSMCB (Korean Society for Molecular and Cellular Biology) news
|
[[media:Media_n_Outreach_001.pdf|기능성유전자 네트워크를 이용한 생물학 연구 (논단)]]

|}
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