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  CSE 590CWi '07:  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, CSE 403 (schematic)
Organizers:  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.
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 Date  Presenters/Participants Topic Details
01/08---- Organizational Meeting ----
01/22Elaine, Rosalia; RuzzoCovariation in RNA AlignmentsDetails
01/29Josh, Pascal; FelsensteinProtein Knot PolynomialsDetails
02/05James, Nguyen; FelsenseteinFunctional Linkage From Correlated Gene LossDetails
02/12Dan, Imran; Noblecis-Regulatory Modules from CHIP2Details
02/26Adrienne, Zizhen; TompaAncestral GenomesDetails
03/05Ben, Elizabeth; RuzzoRNA Homology SearchDetails

 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.  

01/08: ---- Organizational Meeting ----

01/15:   -- Holiday

01/22: Covariation in RNA Alignments -- Elaine, Rosalia; Ruzzo

01/29: Protein Knot Polynomials -- Josh, Pascal; Felsenstein

which improves on the classic paper:

02/05: Functional Linkage From Correlated Gene Loss -- James, Nguyen; Felsensetein

02/12: cis-Regulatory Modules from CHIP2 -- Dan, Imran; Noble

  • VX Jin, A Rabinovich, SL Squazzo, R Green, PJ Farnham, "A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1." Genome Res., 16, #12 (2006) 1585-95. [offcampus]

02/19:   -- Holiday

02/26: Ancestral Genomes -- Adrienne, Zizhen; Tompa

Plus the accompanying Commentary:

03/05: RNA Homology Search -- Ben, Elizabeth; Ruzzo

 Other  Seminars Past quarters of CSE 590C
COMBI & Genome Sciences Seminars
Applied Math Department Mathematical Biology Journal Club
Biostatistics Seminars
Microbiology Department Seminars
Zoology 525, Mathematical Biology Seminar Series

 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: 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
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