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 Tuesdays, 12:45-1:45 PM in BioTech Building Rm 330.

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 2015

Date Presenter Topic/Reading
Jan 20 Organizational Meeting
Jan 27 William Zhang Mouse Genome Analysis Group. "Initial sequencing and comparative analysis of the mouse genome." Nature 420:520-562, 2002. (We will focus on the material on pages 549ff estimating how much of the genome is under selection.)
Feb 3 Nick Jacobs N.G.C. Smith, M. Brandstrom, and H. Hellegren. "Evidence for turnover of functional noncoding DNA in mammalian genome evolution." Genomics 84:806-813, 2004.
Feb 10 Manishi Pandey G. Lunter, C.P. Ponting, and J. Hein. "Genome-wide Identification of Human Functona DNA Using a Neutral Indel Model". PLOS Computational Biology 2(1):e5, 2006.
Feb 17 Yu He B. Gulko, M.J. Hubisz, I. Gronau, and A. Siepel. "A method for calculating probabilities of fitness consequences for point mutations across the human genome". Nature Genetics online publication January 19, 2015.
Feb 26 Jennifer Flynn C.A. Smith, E.J. Want, G. O'Maille, R. Abagyan, and G. Siuzdak. "XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification." Analytical Chemistry 78:779-787, 2006.
Mar 3 William Zhang R. Daly, S. Rogers, J. Wandy, A. Jakevics, K.E.V. Burgess, and R. Breitling. "MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach." Bioinformatics 30(19):2764-2771, 2014.
Mar 10 spring break -- no class
Mar 17 Liron Ganel E.L. Schymanski, M. Gerlich, C. Ruttkies, and S. Neumann. "Solving CASMI 2013 for MetFrag, MetFusion, and MOLGEN-MS/MS." Mass Spectrometry 3(special issue 2):S0036, 2014.
Mar 24 Dennis Wu S. Cortassa, V. Caceres, L.N. Bell, B. O'Rourke, N. Paolocci, and M.A. Aon. "From Metabolomics to Fluxomics: a Computational Procedure to Translate Metabolite Profiles into Metabolic Fluxes." Biophysical Journal 108(1):163-172, 2015.
Mar 31 Xiaojing Huang D.E. Newburger, D. Kashef-Haghighi, Z. Weng, R. Salari, et al. "Genome evolution during progression to breast cancer." Genome Research 23:1097-1108, 2013.
Apr 7 Nicholas Jacobs M. Archetti, D.A. Ferraro, and G. Christofori. "Heterogeneity for IGF-II production maintained by public goods dynamics in neuroendocrine pancreatic cancer." PNAS 112(6): 1833-1838, 2015.
Apr 14 Manishi Pandey K. Yuan, T. Sakoparnig, F. Markowetz, and N. Beerenwinkel. "BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies." Genome Biology 16:36, 2015.
Apr 21 Dennis Wu H. Haeno, M. Gonen, M.B. Davis, J.M. Herman, et al. "Computational modeling of pancreatic cancer reveals kinetics of metastasis suggesting optimum treatment strategies." Cell 148(1-2):362-375, 2012.

Some Prior Editions of the Journal Club