Difference between revisions of "Publications"

Revision as of 01:16, 1 March 2020

• Google Scholar citation report
• Yonsei University Researcher Portal
• 
• '*' First authors; '**' Corresponding authors;

2020

• 88. Lee T*, Lee I** Genome-wide Association Studies in Arabidopsis thaliana: Statistical Analysis and Network-Based Augmentation of Signals Arabidopsis Protocols 4th Ed. Supplementary File submitted

• 87. 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 full text

• 86. 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 full text

• 85. Kim E*, Bae D*, Yang S*, Ko G, Lee S, Lee B**, Lee I**. BiomeNet: A database for construction and analysis of functional interaction networks for any species with a sequenced genome Bioinformatics 2019 Oct 10. pii: btz776 pubmed

• 84. Kim K*, Yang S, Ha SJ, Lee I**, VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data Bioinformatics 2020 Jan 15;36(2):546-551 pubmed

• 83. Shim JE**, Lee I**, Construction of functional protein networks using domain profile associations, Methods in Molecular Biology 2020 Jan;2074:35-44 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. 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 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. 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 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 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.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.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. 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.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.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.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; 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; 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; 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; pubmed

• 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; 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; 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; 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 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. 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 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 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 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 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. 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 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. 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. 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.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.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 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 pubmed

• 49. Shim JE*, Lee I**, Network-assisted approaches for human disease research, Animal Cells and Systems 2015 Aug 19(4):231-235 Link 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 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 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. 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 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 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 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 Pubmed

• 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. 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 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 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 Pubmed

2014 (5)-Sabbatical leave

• 37. Hwang S*, Kim E, Yang S, Marcotte EM*, Lee I**, MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network, Nucleic Acids Res 2014 Jul;42(Web server issue):W147-53. 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. 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 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 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 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 Pubmedpdf

• 31. Lee I** , Network approaches to the genetic dissection of phenotypes in animals and humans. Animal Cells and Systems 2013 17(2)75-79 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 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 pubmed 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 pubmedpdf

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 pubmed 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 pubmedpdf

• 25. Lee I** , Probabilistic functional gene societies. Progress in Biophysics and Molecular Biology 2011 Aug;106(2):435-42 pubmed 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 pubmed 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 pubmed 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 pubmed 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 pubmed 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 pubmed 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 pubmed 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 pubmed 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 pubmed 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 pubmed 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 pubmed 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 pubmed 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 pubmed 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) 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) pubmed 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) pubmed 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) pubmed pdf

• 8. Insuk Lee*, Shailesh V. Date, Alex T. Adai, Edward Marcotte**. A Probabilistic functional network of yeast genes. Science 306:1555-1558, (2004) pubmed 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) pubmed 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)