BIOL 5496/CSE 7800: Computational Molecular Biology Journal Club

Welcome to the home page for BIOL 5496/CSE 7800, the Computational Molecular Biology Journal Club. The Journal Club meets Mondays, 2-3 PM in 4444 Forest Park, Room 6404.

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 Spring 2011

Date Presenter Topic/Reading
Jan 24 Organizational Meeting
Jan 31 Gaurav Singhal A. Mortazavi, B.A. Williams, K. McCue, L. Schaeffer, and B. Wold. "Mapping and quantifying mammalian transcriptomes by RNA-Seq." Nature Methods 5:621-628, 2008.
Feb 7 Chris Schlosberg H. Jiang and W.H. Wong. "Statistical inferences for isoform expression in RNA-Seq." Bioinformatics 25(8):1026-1032, 2009.
Feb 14 Yue Zhao C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van B., S.L. Salzberg, B.J. Wold, and L. Pachter. "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation." Nature Biotechnology 28:511-515, 2010.
Feb 21 Kevin Chen Y. Barash, J.A. Calarco, W. Gao, Q. Pan, X. Wang, O. Shai, B.J. Blencowe, and B.J. Frey. "Deciphering the splicing code." Nature 465:53-59, 2010.
Feb 28 Marc Charbonneau Q. Wang, G. M. Garrity, J. M Tiedje, and J. R Cole. "Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy". Applied and Environmental Microbiology 73(16): 5261-7, 2007.
Mar 7 Molly Gibson W. Li, J.C. Wooley, and A. Godzik. "Probing metagenomics by rapid cluster analysis of very large datasets." PLOS One 3(10):e3375, 2008.
Mar 14 spring break -- no meeting
Mar 21 Vasavi Sundaram C. Lozupone and R. Knight. "UniFrac: a new phylogenetic method for comparing microbial communities." Applied and Environmental Microbiology 71(12):8228-8235, 2005.
Mar 28 Nicholas Ho E. Borenstein, M. Kupiec, M.W. Feldman, and E. Ruppin. "Large-scale reconstruction and phylogenetic analysis of metabolic environments." PNAS 105(38):14482-14487, 2008.
Apr 4 Brett Maricque O. Beja, L. Aravind, E.V. Koonin, M.T. Suzuki, et al. "Bacterial rhodopsin: evidence for a new type of phototrophy in the sea." Science 289:1902-1906, 2000.
Apr 11 no meeting
Apr 18 Adnan Elhammali J.P. Johansen, H. Hamanaka, M.H. Monfils, R. Behnia, K. Deissroth, H.T. Blair, and J.E. LeDoux. "Optical activation of lateral amygdala pyramidal cells instructs associative fear learning." PNAS 107:12692-12697, 2010.
Apr 25 Ben Borgo A. Martinez, A.S. Bradley, J.R. Waldbauer, R.E. Summons, and E.F. DeLong. "Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host." PNAS 104:5590-5595, 2007.
May 2 Zeke Maier M.M. Doroudchi, K.P. Greenberg, J. Liu, K.A. Silka, et al. "Virally delivered Channelrhodopsin-2 safely and effectively restores function in multiple mouse models of blindness." Molecular Therapy advance pub 2011.69, April 2011.

Some Prior Editions of the Journal Club