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, 11 AM - noon 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 Fall 2012

Date Presenter Topic/Reading
Sep 10 Organizational Meeting
Sep 18
Sep 25 Barak Cohen The ENCODE Project Consortium (2012). "An integrated encyclopedia of DNA elements in the human genome." Nature 489:57-74.
Oct 2 Zane Goodwin S Djebali, CA Davis, A Merkel, A Dobin, et al (2012). "Landscape of transcription in human cells." Nature 486:101-108.
Oct 9 Zeke Maier C. Cheng, R. Alexander, R. Min, J. Leng, et al. (2012). Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Research 22:1658-1667.
Oct 16 Nicholas Ho J. Harrow, A. Frankish, J.M. Gonzalez, E. Tapanari, et al. (2012). GENCODE: the reference human genome annotation for the ENCODE project. Genome Research 22:1760-1744.
Oct 23 Shuxiang Ruan M.G. Grabherr, B.J. Haas, M. Yassour, J.Z. Levin, et al. (2011). Full-length transcriptome assembly from RNAseq data without a reference genome. Nature Biotechnology 29:644-652.
Oct 30 Mark Charbonneau C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold, and L. Pachter (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28:511-515.
Nov 6 Hemangi Chaudhari M.H. Schultz, D.R. Zerbino, M. Vingron, and E. Birney (2012). Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28:1086-1092.
Nov 13 Kiersten Ruff J. Chu, R. Lazarus, V.J. Carey, and B.A. Raby (2011). Quantifying differential gene connectivity between disease states for objective identification of disease-relevant genes. BMC Systems Biology 5:89.
Nov 20 Thanksgiving week -- no meeting
Nov 27
Dec 4 Temidayo Adebiyi Y. Sun and S. Goodinson (2009). Optimizing molecular signatures for predicting prostate cancer recurrence. Prostate 69:1119-1127.
Dec 11 Satish Subramanian E. Cosgun, N.A. Limdi, and C.W. Duarte (2011). High-dimensional pharmacogenetic prediction of a continuous trait using machine learning techniques with application to warfarin dose prediction in African Americans. Bioinformatics 27:1384-1389.
Dec 18 Arthur Lee E.R. Greenhill, A. Rocco, L. Vibert, M. Nikaido, and R.N. Kelsh (2011). An iterative genetic and dynamical modelling approach identifies novel features of the gene regulatory network underlying melanocyte development. PLOS Genetics 7:e1002665.

Some Prior Editions of the Journal Club