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 at 10:30 AM in 4515 McKinley, Rm 4212.

Your course masters are Jeremy Buhler and Gary Stormo.

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 2016

Date Presenter Topic/Reading
Aug 29 Organizational Meeting
Sep 5 Labor Day -- no class
Sep 12 Matthew Matlock M Iskar, G Zeller, P Blattmann, M Campillos, et al. Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. Molecular Systems Biology 9:662, 2013.
Sep 19 Tyler Hughes H Yu, J Chen, X Xu, Y Li, et al. A systematic prediction of multiple drug-target interactions from chemical, genomic, and pharmacological data PLOS One 7:e37608, 2012.
Sep 26 Yiming Kang H Noh and R Gunawan. Inferring gene targets of drugs and chemical compounds from gene expression profiles. Bioinformatics 32:2120, 2016.
Oct 3 instructors out -- no class
Oct 10 Lena Dang H Paik, A-Y Chung, H-C Park, RW Park, et al. Repurpose terbutaline sulfate for amyotrophic lateral sclerosis using electronic medical records. Scientific Reports 5:8580, 2015.
Oct 17 Fall Break -- no class
Oct 24 Arnav Moudgil P-R Loh, M Baym, and B Berger. Compressive genomics. Nature Biotechnology 30:627-30, 2012.
Oct 31 Jiayue Liu D Yorukoglu, YW Yu, J Peng, and B Berger. Compressive mapping for next-generation sequencing. Nature Biotechnology 34:374-6, 2016.
Nov 7 Jerry Fong S Sheikhizadeh, ME Schranz, M Akdel, D de Ridder, and S Smit. PanTools: representation, storage, and exploration of pan-genomic data. Bioinformatics 32:i487-i493, 2016.
Nov 14 Brian Leon-Ricardo M Emily, T Mailund, J Hein, L Schauser, and MH Schierup. Using biological networks to search for interacting loci in genome-wide association studies. European Journal of Human Genetics 17:1231-1240, 2009.
Nov 21 Juan Macias BA McKinney, JE Crowe Jr., J Guo, and D Tian. Capturing the spectrum of interaction effects in genetic association studies by simulted evaporative cooling network analysis. PLOS Genetics 5:e1000432, 2009.
Nov 28 Cynthia Ma J Li, JD Malley, AS Andrew, MR Karagas, and JH Moore. Detecting gene-gene interactions using a permutation-based random forest method. BMC BioData Mining 9:14, 2016.
Dec 5 Justin Porter and Aldrin Yim M Gao and J Skolnick. A comprehensive survey of small-molecule binding pockets in proteins. PLOS Computational Biology 9(10):e1003302, 2013.
Dec 12 Alaric D'Souza NM Daniels, A Gallant, J Peng, LJ Cowen, M Baym, and B Berger. Compressive genomics for protein databases. Bioinformatics 29(13):i283-i290, 2013.

Some Prior Editions of the Journal Club