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 Tuesdays, 10:30-11:30 AM in 4515 McKinley, Rm 4212.

Your course masters are Jeremy Buhler and Barak Cohen.

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 2016

Date Presenter Topic/Reading
Jan 21 Organizational Meeting
Jan 26 Brian Leon-Ricardo R Patro, SM Mount, and C Kingsford. "Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms." Nature Biotechnology 32, 462-464, 2014.
Feb 2 Jeremy Buhler H Fan, AR Ives, Y Surget-Groba, and CH Cannon. "An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data." BMC Genomics 16:522, 2015.
Feb 9 Manish Boolchandani DE Wood and SL Salzberg. "Kraken: ultrafast metagenomic sequence classification using exact alignments." Genome Biology 15:R46, 2014.
Feb 16 Kailong Mao C-A Leimeister, M Boden, S Horwege, S Lindner, and B Morgenstern. "Fast alignment-free sequence comparison using spaced-word frequencies." Bioinformatics 30:1991-1999, 2014.
Feb 23 Jerry Fong JN Burton, A Adey, RP Patwardhan, R Qiu, JO Kitzman, and J Shendure. "Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions." Nature Biotechnology 31:1119-1125, 2013.
Mar 1 Barak Cohen E O'Duibhir, P Lijnzaad, JJ Benschop, TL Lenstra, et al. "Cell cycle population effects in perturbation studies." Molecular Systems Biology 10:732, 2014.
Mar 8 Ally Asaro 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.
Mar 15 Spring break -- no class
Mar 22 Jiayue Liu M Hofree, JP Shen, H Carter, A Gross, and T Ideker. "Network-based stratification of tumor mutations." Nature Methods 10:1108-1115, 2013.
Mar 29 Heather Lawson M Chevalier, O Venturelli, and H El-Samad. "The impact of different sources of fluctuations on mutual information in biochemical networks." PLOS Computational Biology 11:e1004462, 2015.
Apr 5 Arnav Moudgil EZ Macosko, A Basu, R Satija, J Nemesh, et al. "Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets." Cell 161:1202-1214, 2015.
Apr 12 Juan Macias A Rotem, O Ram, N Shoresh, RA Sperling, A Goren, DA Weitz, and BE Bernstein. "Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state." Nature Biotechnology 33:1165-1172, 2015.
Apr 19 Aldrin Yim K Achim, J-B Pettit, LR Saraiva, D Gavriouchkina, T Larsson, D Arendt, and JC Marioni. "High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin." Nature Biotechnology 33:503-509, 2015.
Apr 26 Matthew Matlock D Grun, A Lyubimova, L Kester, K Wiebrands, O Basak, N Sasaki, H Clevers, and A van Oudenaarden. "Single-cell messenger RNA sequencing reveals rare intestinal cell types." Nature 525:251-255, 2015.

Some Prior Editions of the Journal Club