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 10:30 AM in 4515 McKinley, Rm 3001C.

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 Spring 2017

Date Presenter Topic/Reading
Jan 26 Organizational Meeting
Feb 2 Nicolette Laird DR Zerbino and E Birney. "Velvet: algorithms for de novo short read assembly using de Bruijn graphs." Genome Research 18(5):821-829, 2008.
Feb 9 Alaric D'Souza Y Peng, HCM Leung, SM Yiu, and FYL Chin. "IBDA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth." Bioinformatics 28:1420-1428, 2012.
Feb 16 Daniel Cui Zhou M Hunt, T Kikuchi, M Sanders, C Newbold, M Berriman, and TD Otto. "REAPR: a universal tool for genome assembly evaluation." Genome Biology 14:R47, 2013.
Feb 23
Mar 2 Kailong Mao Y Tang, E Bouvier, CK Kwok, Y Ding, A Nekrutenko, PC Bevilacqua, and SM Assmann. "StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo." Bioinformatics 31:2668-2675, 2015.
Mar 9 Gary Stormo (Background, no paper assigned)
Mar 16 Spring Break -- no class
Mar 23 Miro Gavin Y Wu, B Shi, X Ding, T Liu, X Hu, KY Yip, ZR Yang, DH Mathews, and ZJ Lu. "Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data." Nucleic Acids Research 43:7247-7259, 2015.
Mar 30 Liang-Bo Wang V Reinharz, F Major, and J Waldispuhl. "Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure." Bioinformatics 28(12):i207-i214, 2012.
Apr 6 Cynthia Ma AM Newman, CL Liu, MR Green, AJ Gentles, W Feng, Y Xu, CD Hoang, M Diehn, and AA Alizadeh. "Robust enumeration of cell subsets from tissue expression profiles. Nature Methods 12:453-457, 2015.
Apr 13 Wenjun Kong W Qiao, G Quon, E Csaszar, M Yu, Q Morris, and PW Zandstra. "PERT: a method of expression deconvolution of human blood samples from varied microenvironmental and developmental conditions." PLOS Computational Biology 8:e1002838, 2012.
Apr 20 Yiming Kang B Li and CN Dewey. "RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome." BMC Bioinformatics 12:323, 2011.
Apr 27 Siqi Zhao AL Sanborn, SSP Rao, S-C Huang, NC Durand, et al. "Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes." PNAS 112(47):E6456, 2015.

Some Prior Editions of the Journal Club