CSE 590C,  Wi '16:  Reading & Research in Comp. Bio.

CSE Home

About Us

Search

Contact Info

Course Info		CSE 590C is a weekly seminar on Readings and Research in Computational Biology, open to all graduate students in computational, biological, and mathematical sciences. When/Where:  Mondays, 3:30 - 4:50, EE1 031 Organizers:  Joe Felsenstein, Sreeram Kannan, Su-In Lee, Bill Noble, Larry Ruzzo, Cole Trapnell Credit:  1-3 Variable Grading:  Credit/No Credit. Talk to the organizers if you are unsure of our expectations.
Email		cse590cb@cs.washington.edu Course-related announcements and discussions   Manage Your Subscription List Archives compbio-seminars@cs.washington.edu Biology seminar announcements from all around campus   Manage Your Subscription List Archives compbio-group@cs.washington.edu Computational biology discussions, conference/job postings, etc.,   Manage Your Subscription List Archives
Schedule		Date  Presenters/Participants Topic Details 01/04 No Class 01/11 ---- Organizational Meeting ---- 01/18 Holiday 01/25 Safiye; Lee Drug discovery Details 02/01 Haoran, Jacob, Kurt; Ruzzo Replication Timing Details 02/08 Ken, Max; Haynor Noncoding variants Details 02/15 Holiday 02/22 Alex, Scott; Felsenstein Population genetic inference Details 02/29 Julien, Sven; Noble Protein contact maps Details 03/07 Jack, Sudipto; Kannan Regulatory code Details
Papers, etc.		Note on Electronic Access to Journals The UW Library is generally a paid subscriber to non-open-access journals we cite. You can freely access these articles from on-campus computers. For off-campus access, follow the "[offcampus]" links below or look at the library "proxy server" instructions. You will be prompted for your UW net ID and password.   01/04:   -- No Class 01/11:   -- ---- Organizational Meeting ---- 01/18:   -- Holiday 01/25: Drug discovery -- Safiye; Lee Bharath Ramsundar, Steven Kearnes, Patrick Riley, Dale Webster, David Konerding, Vijay Pande, Massively Multitask Networks for Drug Discovery: http://arxiv.org/abs/1502.02072 02/01: Replication Timing -- Haoran, Jacob, Kurt; Ruzzo F Liu, C Ren, H Li, P Zhou, X Bo, W Shu, "De novo identification of replication-timing domains in the human genome by deep learning." Bioinformatics, (2015) . [offcampus] 02/08: Noncoding variants -- Ken, Max; Haynor J Zhou, OG Troyanskaya, "Predicting effects of noncoding variants with deep learning-based sequence model." Nat. Methods, 12, #10 (2015) 931-4. [offcampus] 02/15:   -- Holiday 02/22: Population genetic inference -- Alex, Scott; Felsenstein Sara Sheehan, Yun S. Song, Deep learning for population genetic inference: http://biorxiv.org/content/early/2015/10/02/028175 [offcampus] 02/29: Protein contact maps -- Julien, Sven; Noble P Di Lena, K Nagata, P Baldi, "Deep architectures for protein contact map prediction." Bioinformatics, 28, #19 (2012) 2449-57. [offcampus] 03/07: Regulatory code -- Jack, Sudipto; Kannan Basset: Learning the regulatory code of the accessible genome with deep convolutional neural networks. David R Kelley, Jasper Snoek, John Rinn http://biorxiv.org/content/early/2015/10/05/028399 [offcampus]
Other Papers		Other suggested papers that didn't fit the schedule: 1. Alipanahi, Babak, Andrew Delong, Matthew T. Weirauch, and Brendan J. Frey. ``Predicting the Sequence Specificities of DNA- and RNA-Binding Proteins by Deep Learning.'' Nature Biotechnology 33, no. 8 (August 2015): 831--38. doi:10.1038/nbt.3300. http://www.nature.com/nbt/journal/v33/n8/full/nbt.3300.html [offcampus] 2. Zhang, Sai, Jingtian Zhou, Hailin Hu, Haipeng Gong, Ligong Chen, Chao Cheng, and Jianyang Zeng. ``A Deep Learning Framework for Modeling Structural Features of RNA-Binding Protein Targets.'' Nucleic Acids Research, October 13, 2015, gkv1025. doi:10.1093/nar/gkv1025. http://nar.oxfordjournals.org/content/early/2015/10/13/nar.gkv1025 [offcampus] 5. Deep learning of the tissue-regulated splicing code. Leung MK, Xiong HY, Lee LJ, Frey BJ. Bioinformatics. 2014 Jun 15;30(12):i121-9. doi: 10.1093/bioinformatics/btu277. 7. Predicting backbone C-alpha angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network. Lyons J, Dehzangi A, Heffernan R, Sharma A, Paliwal K, Sattar A, Zhou Y, Yang Y. J Comput Chem. 2014 Oct 30;35(28):2040-6. doi: 10.1002/jcc.23718. Epub 2014 Sep 12. https://maxwell.ict.griffith.edu.au/spl/publications/papers/jcc14_lyons.pdf [offcampus]
Other Seminars		Past quarters of CSE 590C COMBI & Genome Sciences Seminars Biostatistics Seminars Microbiology Department Seminars
Resources		Molecular Biology for Computer Scientists, a primer by Lawrence Hunter (46 pages) A Quick Introduction to Elements of Biology, a primer by Alvis Brazma et al. A comprehensive FAQ at bioinformatics.org, including annotated links to online tutorials and lectures. CSE 527: Computational Biology CSEP 590A: Computational Biology (Professional Masters Program) Genome 540/541: Introduction to Computational Molecular Biology: Genome and Protein Sequence Analysis CSE's Computational Molecular Biology research group Interdisciplinary Ph.D. program in Computational Molecular Biology

	Computer Science & Engineering University of Washington Box 352350 Seattle, WA  98195-2350 (206) 543-1695 voice, (206) 543-2969 FAX