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 Thursdays, 3-4 PM in 4444 Forest Park, Room 5507.

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, except for DBBS Computational and Systems Biology students in their first semester, 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 2014

Date Presenter Topic/Reading
Jan 16 Organizational Meeting
Jan 23 Runjun Kumar T. Davoli, A.W. Xu, K.E. Megwasser, L.M. Sack, J.C. Yoon, P.J. Park, and S.J. Elledge. "Cumulative haploinsufficiency and triplosensitivity drive aneuploidy and shape the cancer genome." Cell 155:948-962, 2013.
Jan 30 Sohini Sengupta K-W Tang, B. Alaei-Mahabadi, T. Samuelsson, M. Lindh, and E. Larsson The landscape of viral expression and host gene fusion and adaptation in human cancer Nature Communications 4:2513, 2013.
Feb 6 Manish Boolchandani GP Abel and LB Nuria. Functional impact bias reveals cancer drivers. Nucleic Acids Research 40:e169, 2012.
Feb 13 Manishi Pandey A Nesculea, M Soulillon, M Warnefors, A Liechti, T Daish, U Zeller, JC Baker, F Grutzner, and H Kaessmann. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505:635-640, 2014.
Feb 20 Nicholas Ho AD Ramos, A Diaz, A Nellore, RN Delgado, K-Y Park, G Gonzales-Roybal, MC Oldham, JS Song, and DA Lim. Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell 12:616-628, 2013.
Feb 27 Nicole Rockweiler H van Bakel, C Nislow, BJ Blencowe, and TR Hughes. Most "dark matter" transcripts are associated with known genes. PLoS Biology 8(5):e1000371, 2010.

Please also have a look at a rebuttal of this article and the original authors' reply.

Mar 6 Xiaojing Huang K Struhl. Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nature Structural and Molecular Biology 14:103-105, 2007.
Mar 13 Spring Break -- no meeting
Mar 20 A.A.E. Vinkhuyzen, N.R. Wray, J. Yang, M.E. Goddard, and P.M. Visscher. Estimation and partition of heritability in human populations using whole-genome analysis methods. Annual Reviews of Genetics 47:75-95, 2013.

Background reading includes papers by Weiss and Clark and by Reich and Lander.

Mar 27 T.A. Manolio, F.S. Collins, N.J. Cox, D.B. Goldstein, et al. Finding the missing heritability of complex diseases. Nature 461:747-753, 2009.

E. Eichler, J. Flint, G. Gibson, A. Kong, S.M. Leal, J.H. Moore, and J.H. Nadeau. Missing heritability and strategies forfinding the underlying causes of complex disease. Nature Reviews Genetics 11:446-450, 2010.

Apr 3 Mingchao Xie J.K. Pritchard. Are rare variants responsible for susceptibility to complex diseases? American Journal of Human Genetics 69:124-137, 2001.
Apr 10 Runjun Kumar O. Zuk, E. Hechter, S.R. Sunyaev, and E.S. Lander. The mystery of missing heritability: genetic interactions create phantom heritability. PNAS 109:1193-1198, 2012.
Apr 17 Sohini Sengupta J. Yang, B. Benyamin, P. McEvoy, S. Gordon, et al. Common SNPs explain a large proportion of the heritability for human height. Nature Genetics 42:565-571, 2010.
Apr 24

Some Prior Editions of the Journal Club