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 at 1:30 PM 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.

Announcements of upcoming meetings will be made via the mailing list Please ask one of the course masters if you want to join the list.

Schedule of Presentations for Spring 2018

Date Presenter Topic/Reading
Jan 18 Organizational Meeting
Jan 25 Chris Chermside-Scabbo V Khurana, J Peng, CY Chung, PK Auluck, et al. Genome-scale networks link neurodegenerative disease genes to alpha-synuclein through specific molecular pathways. Cell Systems 4(2):157-170.e14, 2017.
Feb 1 Robert Chen K Drew, CL Müller, R Bonneau, and EM Marcotte. Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets. PLOS Computational Biology 13(10):e1005625, 2017.
Feb 8 Ryan Friedman A Belyaeva, S Venkatachalapathy, M Nagarajan, GV Shivashankar, and C Uhler. Network analysis identifies chromosome intermingling regions as regulatory hotspots for transcription. PNAS 114(52):13714-13719, 2017.
Feb 15 Noah Flynn Y Shen, MJ Alvarez, B Bisikirska, A Lachmann, R Realubit, S Pampou, J Coku, C Karan, and A Califano. Systematic, network-based characterization of therapeutic target inhibitors. PLOS Computational Biology 13(10):e1005599, 2017.
Feb 22 Siqi Zhao NM Mangan, SL Brunton, JL Proctor, and JN Kurtz. Inferring biological networks by sparse identification of nonlinear dynamics. IEEE Transactions on Molecular, Biological, and Multi-Scale Communications 2(1):52-63, 2016.
Mar 1 Nicolette Laird X Ruan, C Wülfing, and RF Murphy. Image-based spatiotemporal causality inference for protein signaling networks. Bioinformatics 33(14):i217-i224, 2017.
Mar 8 Wenjun Kong TE Chan, MPH Stumpf, and AC Babtie. Gene regulatory network inference from single-cell data using multivariate information measures. Cell 5(3):251-267.e3, 2017.
Mar 15 Spring Break -- no class
Mar 22 Kai Loell T Firman, G Balázsi, and K Ghosh. Building predictive models of genetic circuits using the principle of maximum caliber. Biophysical Journal 113(9):2121-2130, 2017.
Mar 29 no class
Apr 5 Paula Godoy R Li, Y Liu, T Li, and C Li. 3Disease Browser: a web server for integrating 3D genome and disease-associated chromosome rearrangement data. Scientific Reports 6:34651, 2016.
Apr 12 Michael Ward GP Way and CS Greene. Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders. Proc. 2018 Pacific Symposium on Biocomputing 80-91, 2018.
Apr 19 Naomi Wilson H Mohimani, W-T Liu, RD Kersten, BS Moore, PC Dorrestein, and PA Pevzner. NRPquest: coupling mass spectrometry and genome mining for nonribosomal peptide discovery. Journal of Natural Products 77:1902-1909, 2014.
Apr 26 Zach Beller A Butler, P Hoffman, P Smibert, E Papalexi, and R Satija. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nature Biotechnology 2018 Apr 2 (Epub ahead of print).

Some Prior Editions of the Journal Club