Publications

2010

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)(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)