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  CSE 590CWi '10:  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 031 (schematic)
Organizers:  Joe Felsenstein, Su-In Lee, Larry Ruzzo, Martin Tompa
Credit: 1-3 Variable
Grading: Credit/No Credit. Talk to the organizers if you are unsure of our expectations.
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 Date  Presenters/Participants Topic Details
01/04---- Organizational Meeting ----
01/11Karl & Elizabeth; RuzzoBinding EnergyDetails
01/25Daniel; TompaConservation & SplicingDetails
02/01Peng; RuzzoHMM SpeedupDetails
02/08Nath & Xiaoyu; Ruzzo5'UTRs from deep seqDetails
02/22Paul & Adrienne; TompaPan-GenomicsDetails
03/01Brendan; FelsensteinAncestral flowering plantsDetails
03/08Andrey, Tsung-chien; LeeNetwork ReconstructionDetails

 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.  

01/04: ---- Organizational Meeting ----

01/11: Binding Energy -- Karl & Elizabeth; Ruzzo

01/18:   -- Holiday

01/25: Conservation & Splicing -- Daniel; Tompa

  • JZ Ni, L Grate, JP Donohue, C Preston, N Nobida, et 5 al., "Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay." Genes Dev., 21, #6 (2007) 708-18. [offcampus]

02/01: HMM Speedup -- Peng; Ruzzo

02/08: 5'UTRs from deep seq -- Nath & Xiaoyu; Ruzzo

02/15:   -- Holiday

02/22: Pan-Genomics -- Paul & Adrienne; Tompa

03/01: Ancestral flowering plants -- Brendan; Felsenstein

03/08: Network Reconstruction -- Andrey, Tsung-chien; Lee

  • E Segal, M Shapira, A Regev, D Pe'er, D Botstein, et 2 al., "Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data." Nat. Genet., 34, #2 (2003) 166-76. [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.
S-Star Bioinformatics Online Course Schedule, a collection of video primers
A very comprehensive FAQ at, 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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University of Washington
Box 352350
Seattle, WA  98195-2350
(206) 543-1695 voice, (206) 543-2969 FAX