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 CSE 590 C, Au '05: 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, MGH 284
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 Papers
10/03   ---- Organizational Meeting ----  
10/10 Zizhen; Larry Cyanobacterial ncRNA Papers
10/17 John; Larry ncRNA Evolution Papers
10/24 Ilya Shmulevich, ISB Modeling Genetic Networks with Probabilistic Boolean Networks Papers
10/31 James, Imran; Martin De novo repeat detection Papers
11/07 Elizabeth; Bill Motif Discovery Papers
11/14 Alex, Jonathan; Joe Tropical Geometry Papers
11/21 Alex, Jonathan; Joe Tropical Geometry Papers
11/28 Amol; Bill Regulatory Modules Papers
12/05 Rosalia, Adrienne; Martin Phylogenetic Shadowing Papers

 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.  

10/03: ---- Organizational Meeting ---- --  

10/10: Cyanobacterial ncRNA -- Zizhen; Larry

10/17: ncRNA Evolution -- John; Larry
There are several recent papers on this topic; we'll focus on the first one below.

10/24: Modeling Genetic Networks with Probabilistic Boolean Networks -- Ilya Shmulevich, ISB

10/31: De novo repeat detection -- James, Imran; Martin

11/07: Motif Discovery -- Elizabeth; Bill

  • Jason Gertz, Linda Riles, Peter Turnbaugh, Su-Wen Ho and Barak A. Cohen, Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics, Genome Research 15:1145-1152, 2005 [offcampus]

11/14: Tropical Geometry -- Alex, Jonathan; Joe

11/21: Tropical Geometry -- Alex, Jonathan; Joe


11/28: Regulatory Modules -- Amol; Bill

  • David C. King, James Taylor, Laura Elnitski, Francesca Chiaromonte, Webb Miller and Ross C. Hardison, Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences, Genome Research 15:1051-1060, 2005 [offcampus]

12/05: Phylogenetic Shadowing -- Rosalia, Adrienne; Martin

 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

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