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 1:00 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 Fall 2018

Date Presenter Topic/Reading
Aug 27 Organizational Meeting
Sep 3 Labor Day -- no meeting
Sep 10 Naomi Wilson C Deneke, R Rentzsch, and BY Renard. PaPrBaG: a machine learning approach for the detection of novel pathogens from NGS data. Scientific Reports 7:39194, 2017.
Sep 17 Dylan Lawrence X Liu, Y Yu, J Liu, CF Elliott, C Qian, and J Liu. A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures. Bioinformatics 34:171-178, 2018.
Sep 24 no meeting
Oct 1 Hannah Bucklin S Nurk, D Meleshko, A Korobeynikov, and PA Pevzner. MetaSPAdes: a new versatile metagenomic assembler. Genome Research 27:824-834, 2017.
Oct 8 Luke Diorio-Toth J Beaulaurier, S Zhu, G Deikus, I Mogno, X-S Zhang, et al. Metgenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature Biotechnology 36:61-69, 2018.
Oct 15 Fall Break -- no meeting
Oct 22 Ariel Hernandez-Levya HT Rube, C Rastogi, JF Kribelbauer, and HJ Bussemaker. A unified approach for quantifying and interpreting DNA shape readout by transcription factors. Molecular Systems Biology 14:e7902, 2018.
Oct 29 Ryan Friedman AM Khamis, O Motwalli, R Oliva, BR Jankovic, YA Medvedeva et al. "A novel method for improved accuracy of transcription factor binding site prediction." Nucleic Acids Research 46:e72, 2018.
Nov 5 Noah Flynn S Giguere, M Marchand, F Laviolette, A Drouin, and J Corbeil. Learnign a peptide-protein binding affinity predictor with kernel ridge regression. BMC Bioinformatics 14:82, 2013.
Nov 12 Pat DeSouza N Abe, I Dror, L Yang, M Slattery, T Zhou, HJ Bussemaker, R Rhohs, and RS Mann. Deconvolving the recognition of DNA shape from sequence. Cell 161:307-18, 2015.
Nov 19 Brittany Smith WM Jacobs and EI Shakhnovich. Structure-Based Prediction of Protein-Folding Transition Paths Biophysical Journal 111:925-936, 2016.
Nov 26 Siqi Zhao
Dec 3 Avi Ramu

Some Prior Editions of the Journal Club