Difference between revisions of "Publications"

Revision as of 14:29, 7 May 2010

Publications (20 total)

• Publications as an Assistant Professor at the Yonsei University, Seoul: 6 total
• Publications as a Postdoctoral Researcher at University of Texas at Austin: 8 total
• Publications as a Graduate Student (MS/PhD): 6 total

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, In press. co-corresponding author
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
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)
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)
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
15. Ben Lehner and Insuk Lee. Network-guided genetic screening: building, testing, and using gene networks to predict gene function. Brief. Funct. Genomic. Proteomic. 7:217-227 (2008). co-corresponding author
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)
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 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).
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)
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)
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)
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)
8. Insuk Lee, Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. Science 306:1555-1558, (2004) 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)
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)

Patents

Community service Associate Editor: Journal Frontiers in Plant Physiology (2010 – present) Editorial Board member: Animal Cells and Systems (2010 – present) Ad hoc Journal reviewer: Genome Research, Genome Biology, Bioinformatics, BioTechniques, IET-Systems Biology, and INFORMS Journal on Computing. Program Committee: ACM Third International Workshop on Data and Text Mining in Bioinformatics (2009) Teaching and Advising University Courses Taught 12. FGP6004 Advanced Bioinformatics, Spring 2010, Yonsei University, Korea 11. BTE7240 Advanced Bioinformatics, Spring 2010, Yonsei University, Korea 10. BTE4402 Bioinformatics, Spring 2010, Yonsei University, Korea 9. UCS1001 Freshmen seminar, Fall 2009, Yonsei University, Korea 8. LSB 3101 Biochemistry I, Fall 2009, Yonsei University, Korea 7. Introduction to Modern Biochemistry, Summer 2009, Yanbian University of Science and Technology, China 6. BTE7240 Advanced Bioinformatics, Spring 2009, Yonsei University, Korea 5. BTE4402 Bioinformatics, Spring 2009, Yonsei University, Korea 4. UCS1001 Freshmen seminar, Fall 2008, Yonsei University, Korea 3. BTE2001 Biochemistry I, Fall 2008, Yonsei University, Korea 3. Introduction to Modern Biochemistry, Summer 2008, Yanbian University of Science and Technology, China 2. BTE7240 Advanced Bioinformatics, Spring 2008, Yonsei University, Korea 1. BTE4402 Bioinformatics, Spring 2008, Yonsei University, Korea

Postdoctoral work Supervised 3. Sohyun Hwang (2010/03 – present) 2. Jungeun Shim (2009/07 – present) 1. Taeyoon Oh (2009/05 – present)

Ph.D. Dissertations Supervised 1. Junha Shin (2008/09 – present)

Masters Theses/Projects Supervised 3. Ara Cho (2009/09 – present) 2. Seongou Ji (2009/09 – present) 1. Hanhae Kim (2009/09 – present)

Invited oral presentations Overseas 20. 2010 Asian Young Researchers Conference on Computational and Omics Biology, National Cheng Kung University, Taiwan (March 11, 2010), Network-guided approaches for genotype-phenotype mapping 19. Department Seminar, Institute of Statistical Science Academia Sinica, Taipei, Taiwan (Mar, 12, 2010), Network-guided approaches for genotype-phenotype mapping 18. Department Seminar, Carnegie Institution of Plant Biology, Stanford, CA, USA (Aug, 28, 2009), Gene Network and Crop Engineering 17. Department Seminar, University of California at Davis, Department of Plant Pathology, Davis, CA, USA (Aug, 27, 2009), Gene network and Crop engineering 16. Department Seminar, Syngenta Global company, R&D center, Research Triangle Park, NC, USA (June 30, 2009) 15. Cold Spring Harbor Laboratory Conference on Plant genomes, Cold Spring Harbor, NY, USA (March 7, 2009) 14. The iPlant Collaborative, Mechanistic modeling grand challenge workshop, Biosphere 2, Tucson, AZ, USA (November 8-9, 2008) 13. Department Seminar, Carnegie Mellon University, Program of Computational Biology, Pittsburg, PA, USA (Jan, 2008) 12. Department Seminar, National Human Genome Research Institute, Bethesda, MD, USA (Jan, 2008) 11. Department Seminar, Rice University, Department of Biochemistry and Cell Biology, Houston, TX, USA (Jan, 2008) 10. Department Seminar, University of Rochester School of Medicine, Department of Medical Genetics, Rochester, NY, USA (Dec, 2007) 9. Cold Spring Harbor Laboratory/Wellcome Trust Conference-Functional Genomics & Systems Biology, Hinxton, UK (Oct. 10-13, 2007) 8. Intelligent Systems for Molecular Biology Conference, Fortaleza, Brazil (Aug. 6-10, 2006) 7. Department Seminar, Indiana University School of Medicine, Center for Computational Biology, Indianapolis, IN, USA (April, 2006) 6. Keystone Symposia, Systems Biology meeting, Taos, NM, USA (Mar. 5-10, 2006) 5. Department Seminar, University of North Carolina at Charlotte, Department of Bioinformatics, Charlotte, NC, USA (Feb, 2006) 4. Institute of Pure and Applied Mathematics (IPAM), Proteomics Reunion Conference, Los Angeles, CA, USA (Dec, 2005) 3. Department Seminar, Monsanto company, St. Louis, MO, USA (Aug, 2005) 2. Intelligent Systems for Molecular Biology Conference, Detroit, MI, USA (June 25-29, 2005) 1. Department Seminar, Rosetta Inpharmatics Inc. Seattle, WA, USA (May, 2005)

Domestic 38. Department Seminar, Chung-Ang University, Department of Life Science, Korea (April 7, 2010) 37. Department Seminar, Ewha Womans University, Division of Molecular & Life Science, Korea (March 23, 2010) 36. Department Seminar, National Cancer Institute, Korea (March 26, 2010) 35. Korean Society for Molecular and Cellular Biology (KSMCB) Systems Biology Symposium, Jeju, Korea (December 4, 2009) 34. Center for Fungal Pathogenesis International Symposium, Seoul, Korea (November 13, 2009) Fungal Genetics and Genomics 33. 2009 Kyungbuk National University Brain Science Center Symposium, Daeku, Korea (November 11, 2009) 32. 2009 International Symposium Commemorating the 200th Anniversary of Darwin’s Birth, Daejeon, Korea (August 21, 2009) Plant genetics using predictive functional gene network model 31. Trilateral Symposium on Systems and Synthetic Biology 2009, Suwon, Korea (August 13-15, 2009), Network-guided Genetics to study complex traits in human and crops 30. Department Seminar, Seoul National University, Integrative biotechnology education program, Korea (May 30, 2009) 29. Department Seminar, Seoul National University, Bio-engineering program, Korea (April 14, 2009) 28. Department Seminar, Korea University, School of Life Sciences and Biotechnology, Korea (April 7, 2009) 27. KHUPO 9th Annual International Proteomics Conference, Seoul, Korea (March 27, 2009), Chair for Functional Proteomics and Systems Biology Symposium 26. Department Seminar, Korea University, National Creative Initiative, Korea (March 18, 2009) 25. The 1st Yonsei Biomedical Forum, Yonsei University, Seoul, Korea (March 11, 2009) 24. Department Seminar, National Institute of Health, Center for Genome Science, Korea (November 19, 2008) 23. Department Seminar, Seoul National University, School of Biological Science, Korea (November 17, 2008) 22. The 9th international conference of Korean Society for Bioinformatics and Systems Biology (KSBSB), Chungbuk National University, Korea (November 13-14, 2008) 21. International symposium on systems bioinformatics, Iwha Women’s University, Korea (November 12, 2008) 20. International Meeting of the Federation of Korean Microbiological Societies, Seoul KyoYuk MunHwa HoeKwan, Seoul, Korea (October 16-17, 2008) 19. The 8th KIAS-Yonsei Conference on Protein Structure and Function, Yonsei University, Korea (October 9-11, 2008) 18. 2008 Fall KSBB Meeting and International Symposium, Jeju ICC, Korea (October 6-7, 2008) 17. Korean Society of Medical Biochemistry and Molecular Biology (KSMBMB) 2008 Summer conference, Jeong-dong-jin, Korea (July 10-12, 2008) 16. 1st International Symposium of Global 5-5-10 Yonsei Biomedical Science and Technology Initiative, Seoul, Korea (June 28, 2008) 15. The Korean Society for Microbiology and Biotechnology (KMB) 2008 International Symposium and Annual Meeting, Seoul, Korea (June 26-28, 2008) 14. Department Seminar, Soong-sil University, Department of Bioinformatics, Seoul, Korea (June 1, 2008) 13. The Korean Human Proteome Organization (KHUPO) 8th Annual International Proteomics Conference, Jeju, Korea (May 29-31, 2008) 12. Department Seminar, Korea University, Bioinformatics association, Seoul, Korea (April, 2008) 11. Department Seminar, Yonsei University, Institute of Life science and Biotechnology, Seoul, Korea (April, 2008) 10. Department Seminar, Yonsei University, Department of Biotechnology, Seoul, Korea (Mar, 2008) 9. Department Seminar, Pochon Cha University College of medicine, Seoul, Korea (Sept, 2007) 8. Department Seminar, Myongji University, Department of Life Science, Suwon, Korea (Sept, 2007) 7. Department Seminar, Yeungnam University, Department of Life Science, Daegu, Korea (Sept, 2007) 6. Department Seminar, Pohang University of Science and Technology (POSTECH), School of Interdisciplinary Bioscience and Bioengineering, Pohang, Korea (Sept, 2007) 5. Department Seminar, Seoul National University, College of Agriculture and Life Science, Seoul, Korea (Sept, 2007) 4. Department Seminar, Hanyang University, Department of Life Science, Seoul, Korea (Sept, 2007) 3. Department Seminar, Sungshin Women’s University, Department of Life Science, Seoul, Korea (Sept, 2007) 2. Solanaceae Genomics meeting, Jeju, Korea (Sept. 9-13, 2007) 1. Department Seminar, Pohang University of Science and Technology (POSTECH), Department of Life Science, Pohang, Korea (Mar, 2006) -->