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 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 2021

Date Presenter Topic/Reading
Aug 30 Organizational Meeting
Sep 6 Labor Day -- no meeting
Sep 13 Marie Crane J Ghurye, T Treangen, M Fedarko, WJ Hervey IV, and M Pop. "MetaCarvel: linking assembly graph motifs to biological variants. Genome Biology 20:174, 2019.
Sep 20 Travis Law H Li, X Feng, and C Chu. "The design and construction of reference pangenome graphs with minigraph." Genome Biology 21:265, 2020.
Sep 27 Doug Abrams / Emily Benedict RM Colquhoun, MB Hall, L Lima, LW Roberts, et al. "Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs." Genome Biology 22:267, 2021.
Oct 4 Dian Li I Minkin and P Medvedev. "Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ." Nature Communications 11:6327, 2020.
Oct 11 Fall break -- no meeting
Oct 18 Isaac Plutzer V Demichev, P Tober-Lau, O Lemke, M Ralser, F Kurth, et al. "A time-resolved proteomic and prognostic map of COVID-19." Cell Systems 12(8):780-794, 2021.
Oct 25 John Wildenthal
Nov 1 Colin McCornack / Borna Novak
Nov 8 Bridget Phillips Alignment-free Comparison and Pseudoalignment
Nov 15 Prashant Kuntala
Nov 22 Wenjin Zhang Fine-tuning Gene Network Models with Single-Cell Data
Nov 29 Megan Burkhalter / Steven Hartman
Dec 6 Chia-Jung Lee
Dec 13 Clara Liu

Some Prior Editions of the Journal Club