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  CSE 590CWi '12:  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, EEB 054 (schematic)
Organizers:  Elhanan Borenstein, Joe Felsenstein, Bill Noble, Larry Ruzzo, Martin Tompa
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
01/09---- Organizational Meeting ----
01/16Holiday
01/23C.Miles; JoeEvolutionary Trajectories in Fitness LandscapesDetails
01/30Elizabeth; ElhananGene Transfer in MicrobiomesDetails
02/06John; Bill & Larrycis-Regulatory Modules and EnhancersDetails
02/13Evan, Daniel; MartinSelection For Overlapping FunctionsDetails
02/20Holiday
02/27Ezgi; LarryParallel de Bruijn AssemblyDetails
03/05Max; BillNon-unique read mapping in ChIPseq for TFBS discoveryDetails

 Papers, etc.

  Note on Electronic Access to Journals

Links to full papers below are often to journals that require a paid subscription. The UW Library is generally a paid subscriber, and you can freely access these articles if you do so from an on-campus computer. 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 once per session.  


01/09: ---- Organizational Meeting ----

01/16:   -- Holiday

01/23: Evolutionary Trajectories in Fitness Landscapes -- C.Miles; Joe

01/30: Gene Transfer in Microbiomes -- Elizabeth; Elhanan

And/or:

02/06: cis-Regulatory Modules and Enhancers -- John; Bill & Larry

02/13: Selection For Overlapping Functions -- Evan, Daniel; Martin

  • MF Lin, P Kheradpour, S Washietl, BJ Parker, JS Pedersen, M Kellis, "Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes." Genome Res., 21, #11 (2011) 1916-28. [offcampus]

02/20:   -- Holiday

02/27: Parallel de Bruijn Assembly -- Ezgi; Larry

03/05: Non-unique read mapping in ChIPseq for TFBS discovery -- Max; Bill

  • D Chung, PF Kuan, B Li, R Sanalkumar, K Liang, EH Bresnick, C Dewey, S KeleĊŸ, "Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data." PLoS Comput. Biol., 7, #7 (2011) e1002111. [offcampus]

 Other  Seminars Past quarters of CSE 590C
COMBI & Genome Sciences Seminars
Applied Math Department Mathematical Biology Journal Club
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 very comprehensive FAQ at bioinformatics.org, including annotated references to online tutorials and lectures.
CSE 527: Computational Biology
CSE 590TV/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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