Difference between revisions of "Publications"

Revision as of 10:46, 17 November 2015

• Google Scholar citation report
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• '*' co-corresponding authorship

2016 (1)

• 51. Eiru Kim, Sohyun Hwang, Hyojin Kim, Hongseok Shim, Byunghee Kang, Sunmo Yang, Jae Ho Shim, Seung Yeon Shin, Edward M. Marcotte and Insuk Lee MouseNet v2: A database of gene networks for studying the laboratory mouse and eight other model vertebrates,Nucleic Acids Research 2016 In press

2015 (13)

• 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 pubmed0
• 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-asisted 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 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)

• 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. Ara Cho, Junha Shin, Sohyun Hwang, Chanyoung Kim, Hongsuk Shim, Hyojin Kim, Hanhae Kim, Insuk Lee, WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans, Nucleic Acids Res. 2014 Jul;42(Web Server issue):W76-82 Pubmed
• 34. Junha Shin, Tak Lee, Hanhae Kim and Insuk Lee, Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. Mol. BioSyst., 2014 Jan;10(1):24-9 Pubmed
• 33. Hanhae Kim, Junha Shin, Eiru Kim, Hyojin Kim, Sohyun Hwang, Jung Eun Shim, Insuk Lee, YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. Nucleic Acids Research 2014 Jan;42(Database issue):D731-6 Pubmed

2013 (2)

• 32. Eiru Kim, Hanhae Kim and Insuk Lee, 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. Insuk Lee, 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. Peggy I Wang, Sohyun Hwang, Rodney P Kincaid, Christopher S Sullivan, Insuk Lee*, and Edward M Marcotte*. RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. Genome Biology 13:R125 (2012)pubmed
• 29. Lee Chae*, Insuk Lee*, Junha Shin, and Seung Yon Rhee*. Towards understanding how molecular networks evolve in plant. Current Opinion in Plant Biology 15:177-184 (2012)pubmed pdf
• 28. Stephanie M. Quanbeck, Libuse Brachova, Alexis A. Campbell, Xin Guan, Ann Perera, Kun He, Seung Y. Rhee, Preeti Bais, Julie A. Dickerson, Philip Dixon, Gert Wohlgemuth, Oliver Fiehn, Lenore Barken, Iris Lange, B. Markus Lange, Insuk Lee, Diego Cortes, Carolina Salazar, Joel Shuman, Vladimir Shulaev, David V. Huhman, Lloyd W. Sumner, Mary R. Roth, Ruth Welti, Hilal Ilarslan, Eve S. Wurtele, and Basil J. Nikolau. Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of “unknown function”. Frontiers in Plant Science 3:1-12 (2012) pubmedpdf

2011 (5)

• 27. Insuk Lee*, Young-Su Seo, Dusica Coltrane, Sohyun Hwang, Taeyun Oh, Edward M. Marcotte*, and Pamela C. Ronald*. Genetic dissection of the biotic stress response using a genome-scale gene network for rice. PNAS 108(45):18548-53 (2011) pubmed pdf

• 26. Sohyun Hwang, Seung Y. Rhee*, Edward M. Marcotte*, and Insuk Lee*. Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana. Nature Protocols 6:1429-1442 (2011) pubmedpdf

• 25. Insuk Lee, Probabilistic functional gene societies. Progress in Biophysics and Molecular Biology 106:435-442 (2011) pubmed pdf

• 24. Insuk Lee*, U. Martin Blom, Peggy I. Wang, Jung Eun Shim, and Edward M. Marcotte*. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Research 21:1109-1121 (2011) pubmed pdf

• 23. Young-Su Seo, Mawsheng Chern, Laura E. Bartley, Muho Han, Ki-Hong Jung, Insuk Lee, Harkamal Walia, Todd Richter, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E. Canlas, Randy Ruan, Chang-Jin Park, Xuewel Chen, Sohyun Hwang, Jong-Seong Jeon, and Pamela C. Ronald. Towards establishment of a rice stress response interactome. PLoS Genetics 7(4):e1002020 (2011) pubmed pdf

2010 (4)

• 22. Ni Huang, Insuk Lee, Edward M.Marcotte, Matthew E.Hurles, Characterising and predicting haploinsufficiency in the human genome, PLoS Genet. 6(10):e1001154(2010) pubmed pdf

• 21. Eiru Kim, Jaeyoon Shin and Insuk Lee, Assessment of effectiveness of the network-guided genetic screen, Mol Biosyst. 6:1803-1806(2010) pubmed pdf

• 20. Insuk Lee*, Ben Lehner, Tanya Vavouri, Junha Shin, Andrew G. Fraser, and Edward M. Marcotte, Predicting genetic modifier loci using functional gene networks, Genome Research, 20:1143-1153(2010) . co-corresponding author pubmed pdf

• 19. Insuk Lee*, Bindu Ambaru, Pranjali Thakkar, Edward M Marcotte*, Seung Y Rhee*, Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana, Nature Biotechnology, 28:149-156 (2010). co-corresponding author pubmed pdf

2009 (3)

• 18. Insuk Lee and Edward Marcotte. Effects of functional bias on supervised learning of a gene network model. In Methods in Molecular Biology Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. p463-475 (2009) pubmed pdf

• 17. Zhihua Li, Insuk Lee, Emily Moradi, Nai-Jung Hung, Arlen W. Johnson, Edward M. Marcotte, Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, PLoS Biology, 7(10):e1000213 (2009) pubmed pdf

• 16. Ryan S. Gray, Philip B. Abitua, Bogdan J. Wlodarczyk, Heather L. Szabo-Rogers, Otis Blanchard, Insuk Lee, Greg S. Weiss, Karen J. Liu, Edward M. Marcotte, John B. Wallingford, Richard H. Finnell. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, Nature Cell Biology 11:1225-32 (2009) *Cover story pubmed pdf

2008 (3)

• 15. Ben Lehner* and Insuk Lee*. Network-guided genetic screening: building, testing, and using gene networks to predict gene function. Brief. Funct. Genomic. 7:217-227 (2008). co-corresponding author pubmed pdf

• 14. Insuk Lee and Edward Marcotte. Integrating Functional Genomics Data. In Methods in Molecular Biology Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. p267-278 (2008) pubmed pdf

• 13. Insuk Lee, Ben Lehner, Catriona Crombie, Wendy Wong, Andrew G. Fraser, Edward M. Marcotte. A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nature Genetics 40:181-188 (2008). *Cover story 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)