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 at 10:30 AM 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 2017

Date Presenter Topic/Reading
Aug 29 Organizational Meeting
Sep 5 Jeff Hansen MJ Chaisson and G Tesler. "Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory." BMC Bioinformatics 13:238, 2012.
Sep 12 Dan Cui Zhou K Berlin, S Koren, C-S Chin, JP Drake, JM Landolin, and AM Phillippy. "Assembling large genomes with single-molecule sequencing and locality-sensitive hashing." Nature Biotechnology 33:623-630, 2015.
Sep 19 Zach Beller MJ Chaisson, J Huddleston, MY Dennis, MH Sudmant, et al. "Resolving the complexity of the human genome using single-molecule sequencing." Nature 517:608-611, 2015.
Sep 26 Chris Chermside-Scabbo D Sharon, H Tilgner, F Grubert, and M Snyder. "A single-molecule long-read survey of the human transcriptome." Nature Biotechnology 31:1009-1014, 2013.
Oct 3 Robert Chen S Yousefi, F Amrollahi, M Amgad, C Dong, JE Lewis, C Song, DA Gutman, SH Halani, JE Velazquez-Vega, DJ Brat, and LAD Cooper. "Predicting clinical outcomes from large scale cancer genomic profiles with deep survival models." Nature Scientific Reports 7:11707, 2017.
Oct 10 Jeremy Buhler B Lee, J Baek, S Park, and S Yoon. "DeepTarget: end-to-end learning framework for microRNA prediction using deep recurrent neural networks." Proc. ACM Conference on Bioinformatics and Computational Biology 434-442, Oct 2016.
Oct 17 Fall Break -- no class
Oct 24 Liang-Bo Wang OZ Kraus, JL Ba, and BJ Frey. "Classifying and segmenting microscopy images with deep multiple instance learning." Bioinformatics 32:i52-i59, 2016.
Oct 31 Mike Toomey R Singh, J Lanchantin, G Robins, and Y Qi. "DeepChrome: deep-learning for predicting gene expression from histone modifications." Bioinformatics 32:i639-i648, 2016.
Nov 7 Yiming Kang M Hofree, JP Shen, H Carter, A Gross, and T Ideker. "Network-based stratification of tumor mutations." Nature Methods 10:1108-1115, 2013.
Nov 14 Nicolette Laird A Javed, S Agrawal, and PC Ng. "Phen-Gen: compbining phenotype and genotype to analyze rare disorders." Nature Methods 11:935-937, 2014.
Nov 21 Thanksgiving week -- no meeting
Nov 28 Cynthia Ma AM Mezlini and A Goldenberg. "Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases." PLOS Computational Biology 13(10):e1005580, 2017.
Dec 5 Miro Gavin B Cleary, L Cong, A Cheung, ES Lander, and A Regev. "Efficient generation of transcriptomic profiles by random composite measurements." Cell 171 (in press), 2017.

Some Prior Editions of the Journal Club