BIOL 5496/CSE 780x: Computational Molecular Biology Journal Club

Welcome to the home page for BIOL 5496/CSE 780x, the Computational Molecular Biology Journal Club. The Journal Club meets Mondays at 4:45 PM in the Center for Genome Sciences Classroom, 4444 Forest Park Room 5206.

Your course masters are Jeremy Buhler and Barak Cohen.

Participants in the Journal Club present recent published research in the areas of computational molecular biology, systems biology, and bioinformatics. Every student receiving credit for participation must present a paper at one meeting of the Journal Club and must otherwise participate as described in the course overview. Other students, postdocs, faculty, and staff are welcome to attend and participate.

Schedule of Presentations for Fall 2010

Date Presenter Topic/Reading
Sep 13 Organizational Meeting
Sep 20 Chris Fiore S. Sindi, E. Helman, A. Bashir, and B. Raphael. "A geometric approach for classification and comparison of structural variants." Bioinformatics 25(12):i222-i230, 2009.
Sep 27 Brett Maricque R. Satija, J. Hein, and G. Lunter. "Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques." Bioinformatics 26(17):2116-2120, 2010.
Oct 4 Molly Gibson I. Hajirasouliha, F. Hormozdiari, C. Alkan, J. Kidd, I. Birol, E. Eichler, and S.C. Sahinalp. "Detection and characterization of novel sequence insertions using paired-end next-generation sequencing." Bioinformatics 26(10):1277-1283, 2010.
Oct 11 Yue Zhao S.T. Reddy, X. Ge, A. Miklos, R. Hughes, S. Kang, K. Hoi, C. Chrysostomou, S. Hunicke-Smith, B. Iverson, P. Tucker, A. Ellington and G. Georgiou. "Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells." Nature Biotechnology 28:965-969, 2010.
Oct 18 Vasavi Sundaram N. Kaplan, I. Moore, Y. Fondufe-Mittendorf, A. Gossett, D. Tillo, Y. Field, E. LeProust, T. Hughes, J. Lieb, J. Widom, and E. Segal. "The DNA-encoded nucleosome organization of a eukaryotic genome." Nature 458:362-366, 2009.
Oct 25 Mark Charbonneau Y. Zhang, Z. Moqtaderi, B.P. Rattner, G. Euskirchen, M. Snyder, J.T. Kadonaga, X.S. Liu, and K. Struhl. "Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo". Nature Structural and Molecular Biology 16:746-852, 2009.
Nov 1 Kevin Chen M.A. Beer and S. Tavazoie. "Predicting Gene expression from Sequence." Cell 117(2):185-198, 2004.
Nov 8 no meeting this week
Nov 15 Nicholas Ho T.Y.-C. Tsai, Y.S. Choi, W. Ma, J.R. Pomerening, C. Tang, and J.E. Ferrell, Jr. "Robust, tunable biological oscillations from interlinked positive and negative feedback loops." Science 321:126-129, 2008.
Nov 22 Igor Nikolskiy J. Rodrigues and A. Wagner. "Evolutionary plasticity and innovations in complex metabolomic reaction networks." PLoS Computational Biology 5:e1000613, 2009.
Nov 29 no meeting this week
Dec 6 Adnan Elhammali N.E. Lewis, G. Schramm, A. Bordbar, J. Schellenberger, M.P. Andersen, J.K. Cheng, N. Patel, A. Yeee, R.A. Lewis, R. Eils, R. Konig, and B.O. Palsson. "Large-scale in-silico modeling of metabolic interactions between cell types in the human brain." Nature Biotechnology advance online publicaton, Nov 21, 2010.
Dec 13 Gaurav Singhal C. C. Guet, M. B. Elowitz, W. Hsing, and S. Leibler. "Combinatorial synthesis of genetic networks." Science 296:1466-1470, 2002.

Some Prior Editions of the Journal Club