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 10:00 AM on Zoom. Please see our Canvas site or the compgen-disc mailing list for the Zoom link.

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 Fall 2020

Date Presenter Topic/Reading
Sep 14 Organizational Meeting
Sep 21 Erik Storrs E Becht, L McInnes, J Healy, C-A Dutertre, IWH Kwok, LG Ng, F Ginhoux, and EW Newell. "Dimensionality reduction for visualizing single-cell data using UMAP." Nature Biotechnology 37:38-44, 2019.
Sep 28 Yom Kippur - no meeting
Oct 5 Aidan Schneider AH Williams, TH Kim, F Wang, S Vyas, SI Ryu, KV Shenoy, M Schnitzer, TG Kolda, and S Ganguli. "Unsupervised Discovery of Demixed, Low-Dimensional Neural Dynamics across Multiple Timescales through Tensor Component Analysis." Neuron 98(6):1099-1115.e8, 2018.
Oct 12 Nathan Walmsley Z Yang and G Michailidis. "A non-negative matrix factorization method for detecting modules in heterogeneous omics multi-modal data." Bioinformatics 32(1):1-8, 2016.
Oct 19 Travis Law C Xia, J Fan, G Emanuel, J Hao, and X Zhaung. "Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression." PNAS 116:19490-19499, 2019.
Oct 26 Steven Hartman RU Sheth, M Li, W Jiang, PA Sims, KW Leong, and HH Wang. "Spatial metagenomic characterization of microbial biogeography in the gut." Nature Biotechnology 37:877-883, 2019.
Nov 2 Junedh Amrute R Satija, JA Farrell, D Gennert, AF Schier, and A Regev. Spatial reconstruction of single-cell gene expression data. Nature Biotechnology 33:495-502, 2015.
Nov 9 Isaac Plutzer PMJ Beltran, RA Mathias, and IM Cristea. "A portrait of the human organelle proteome in space and time during cytomegalovirus infection." Cell Systems 3(4):371-373.e6, 2016.
Nov 16 Marie Crane B Linard, K Swenson, and F Pardi. "Rapid alignment-free phylogenetic identification of metagenomic sequences." Bioinformatics 35(18):3303-3312, 2019.
Nov 23 Thanksgiving week -- no meeting
Nov 30 Max Bernstein CR de Pierri, R Voyceik, LGCS de Mattos, MG Kulik, et al. "SWeeP: representing large biological sequences datasets in compact vectors." Scientific Reports 10:91, 2020.
Dec 7 Jeremy Buhler (?)
Dec 14

Some Prior Editions of the Journal Club