Schedule

January 12, 2004
Presenter: Julie Kim
Article: Gael Yvert, Rachel B Brem, Jacqueline Whittle, Joshua M Akey, Eric Foss, Erin N Smith, Rachel Mackelprang & Leonid Kruglyak, "Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors," Nature Genetics, v. 35 n. 1 (September 2003): 57-64.

January 19, 2004 - Cancelled (MLK Holiday)

January 26, 2004
Presenter: Carlos Santos
Article: Benjamin P. Lewis, I-hung Shih, Matthew W. Jones-Rhoades, David P. Bartel,and Christopher B. Burge, "Prediction of Mammalian MicroRNA Targets," Cell, Vol. 115, (December 26, 2003): 787–798.

February 2, 2004
Presenter: Rich McEachin
Article: Jodi M Maglich, Ann Sluder, Xiaojun Guan, Yunling Shi, David D McKee, Kevin Carrick, Kim Kamdar, Timothy M Willson, John T Moore, "Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes," Genome Biology, 2(8) (2001): research0029.1–0029.7

February 9, 2004
Presenter: Arvind Rao
Article: Eran Segal, Michael Shapira, Aviv Regev, Dana Pe'er, David Botstein,
Daphne Koller, Nir Friedman, "Module networks: identifying regulatory modules and their condition specific regulators from gene expression data," Nature Genetics, v.34, n.2, (2003): 166-176.

February 16, 2004
Presenter: Viktoriya Strumba
Article: Joshua M. Stuart, Eran Segal, Daphne Koller, and Stuart K. Kim, "A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules," Science, v.302, (2003): 249-255.

February 23, 2004 - Cancelled (Winter Recess)

March 1, 2004
Presenter: Jayson Falkner Tom Blackwell
Article: Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller and David J. Lipman, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs," Nucleic Acids Research, v.25, n.17, (1997): 3389-3402.

March 8, 2004
Presenter: Reagan Kelly
Article: Jonathan E. Allen, Mihaela Pertea, and Steven L. Salzberg, "Computational Gene Prediction Using Multiple Sources of Evidence," Genome Research, v.14, (2004): 142-148

March 15, 2004
Presenter: Shankar Subramanian
Article: Pedro Gonnet and Frederique Lisacek, "Probabilistic alignment of motifs with sequences," Bioinformatics, v. 18, n. 8 (2002): 1091-1101.

March 22, 2004
Presenter: Xing Li
Article: Ziv Bar-Joseph, Georg K Gerber, Tong Ihn Lee, Nicola J Rinaldi, Jane Y Yoo, Francois Robert, D Benjamin Gordon, Ernest Fraenkel, Tommi S Jaakkola, Richard A Young and David K Gifford, "Computational discovery of gene modules and regulatory networks," Nature Biotechnology v. 21, n.11 (2003): 1337-1342.

March 29, 2004
Presenter: Dan Rhodes
Article: L. Giot, J. S. Bader, C. Brouwer, A. Chaudhuri, B. Kuang, Y. Li, Y. L. Hao, C. E. Ooi, B. Godwin, E. Vitols, G. Vijayadamodar, P. Pochart, H. Machineni, M. Welsh, Y. Kong, B. Zerhusen, R. Malcolm, Z. Varrone, A. Collis, M. Minto, S. Burgess, L. McDaniel, E. Stimpson, F. Spriggs, J. Williams, K. Neurath, N. Ioime, M. Agee, E. Voss, K. Furtak, R. Renzulli, N. Aanensen, S. Carrolla, E. Bickelhaupt, Y. Lazovatsky, A. DaSilva, J. Zhong, C. A. Stanyon, R. L. Finley, Jr., K. P. White, M. Braverman, T. Jarvie, S. Gold, M. Leach, J. Knight, R. A. Shimkets, M. P. McKenna, J. Chant, and J. M. Rothberg, "A Protein Interaction Map of Drosophila melanogaster," Science v. 302, (2003): 1727-1736.

April 5, 2004
Presenter: Paveena Lertampaiporn
Article: Eleanor J. Gardiner, Peter Willett, and Peter J. Artymiuk, "Protein Docking Using a Genetics Algorithm," PROTEINS: Structure, Function and Genetics v.44 (2001): 44-56

April 12, 2004
Presenter: Ji Chen Yu Chen
Article: Motonori Ota, Kengo Kinoshita, Ken Nishikawa, "Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile and sequence conservation," J. Mol. Biol. 327.5 (2003): 1053 - 1064.

April 19, 2004
Presenter: Jayson Falkner
Article: Jan Eriksson and David Fenyo, "Probity: a protein identification algorithm with accurate assignment of the statistical significance of the results," J. Proteome Res. 3.1 (2004): 32 - 36