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  CSE 590CWi '16:  Reading & Research in Comp. Bio.
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 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
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compbio-group@cs.washington.edu Computational biology discussions, conference/job postings, etc.,
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 Schedule
 Date  Presenters/Participants Topic Details
01/04No Class
01/11---- Organizational Meeting ----
01/18Holiday
01/25Safiye; LeeDrug discoveryDetails
02/01Haoran, Jacob, Kurt; RuzzoReplication TimingDetails
02/08Ken, Max; HaynorNoncoding variantsDetails
02/15Holiday
02/22Alex, Scott; FelsensteinPopulation genetic inferenceDetails
02/29Julien, Sven; NobleProtein contact mapsDetails
03/07Jack, Sudipto; KannanRegulatory codeDetails
 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┬ánovo identification of replication-timing domains in the human genome by deep learning." Bioinformatics, (2015) . [offcampus]

02/08: Noncoding variants -- Ken, Max; Haynor

02/15:   -- Holiday

02/22: Population genetic inference -- Alex, Scott; Felsenstein

02/29: Protein contact maps -- Julien, Sven; Noble

03/07: Regulatory code -- Jack, Sudipto; Kannan

 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


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