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, 3:00-4:00 PM in 4444 Forest Park Rm 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 2015

Date Presenter Topic/Reading
Aug 27 Organizational Meeting
Sep 3 Dennis Wu J Barretina, G Caponigro, N Stransky, K Venkatesan, et al. The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity. Nature 483:603-607, 2012.
Sep 10 Liron Ganel NP Tobin, JC Harrell, J Lovrot, S Egyhazi Brage, et al. Molecular subtype and tumor characteristics of breast cancer metastases as assessed by gene expression significantly influence patient post-relapse survival. Annals of Oncology 26:81-88, 2015.
Sep 17 Barak Cohen M Kircher, DM Witten, P Jain, BJ O'Roark, GM Cooper, and J Shendure. A general framework for estimating the relative pathogenicity of human genetic variants. Nature Genetics 46:310-315, 2014.
Sep 24 Lena Dang TS Gujral, L Peshkin, and MW Kirschner. Exploiting polypharmacology for drug target deconvolution. PNAS 111:5048-5053, 2014.
Oct 1 Nick Jacobs CR Weinberg, M Shi, LA DeRoo, JA Taylor, DP Sandler, and DM Umbach. Asymmetry in family history implies nonstandard genetic mechanisms: appplication to the genetics of breast cancer. PLoS Genetics 10(3):e1004174, 2014.
Oct 8 Ally Asaro G Hannum, J Guinney, L Zhao, L Zhang, et al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Molecular Cell 49:359-367, 2013.
Oct 15 Jennifer Flynn C Knothe, A Doehring, A Ultsch, and J Lotsch. Methadone induces hypermethylation of human DNA. Epigenomics advance publication 10.2217/epi.15.78, 2015.
Oct 22 Yu He N Rajagopal, W Xie, Y Li, U Wagner, W Wang, J Stamatoyannopoulos, J Ernst, M Kellis, and B Ren. RFECS: a random-forest based algorithm for enhancer identification from chromatin state. PLOS Computational Biology 9:e1002698, 2013.
Oct 29 Jeremy Buhler H Li and N Homer. A survey of sequence alignment algorithms for next-generation sequencing. Briefings in Bioinformatics 11:473-483, 2010.
Nov 5 Dennis Wu B Langmead, C Trapnell, M Pop, and SL Salzberg. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25, 2009.
Nov 12 Thomas Pranzatelli M Pertea, GM Pertea, CM Antonescu, T-C Chang, JT Mendell, and SL Salzberg. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33:290-295, 2015.
Nov 19 Tyler Hughes C Coarfa, F Yu, CA Miller, Z Chen, RA Harris, and A Milosavljevic. Pash 3.0: a versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. BMC Bioinformatics 11:572, 2010.
Nov 26 Thanksgiving break -- no class
Dec 3 William Zhang A Tero, S Takagi, T Saigusa, K Ito, DP Bebber, MD Fricker, K Yumiki, R Kobayashi, and T Nakagaki. Rules for biologically inspired adaptive network design. Science 327:439-442, 2010.

Some Prior Editions of the Journal Club