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  CSE 590CAu '11:  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 026 (schematic)
Organizers:  Elhanan Borenstein, Joe Felsenstein, Su-In Lee, 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
10/03---- Organizational Meeting ----
10/10Daniel; TompaPrimate exome sequencingDetails
10/17Miles; RuzzoNon-coding variationDetails
10/24Elizabeth; NobleSelection and nucleosome positioningDetails
10/31Michael; FelsensteinNetwork ArchaeologyDetails
11/07Sam; TompamiRNA targets in repetitive coding sequenceDetails
11/14Ajit; RuzzoGibbs sampling for RNA predictionDetails
11/21Dr. Jesse Bloom, FHCRCThe role of epistasis in protein and viral evolution 
11/28Max; NobleMore on nucleosome positioningDetails
12/05John; BorensteinSimplicity in metabolic networksDetails

Fall schedule is now filled. FYI, here are the other papers that were suggested.

Borenstein (both; one is a short revew of the other):

Felsenstein (either or both):
Noble (another on nucleosome (re-)positioning).

 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: Primate exome sequencing -- Daniel; Tompa

  • RD George, G McVicker, R Diederich, SB Ng, AP Mackenzie, WJ Swanson, J Shendure, JH Thomas, "Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection." Genome Res, 21, #10 (2011) 1686-1694. [offcampus]

10/17: Non-coding variation -- Miles; Ruzzo

10/24: Selection and nucleosome positioning -- Elizabeth; Noble

  • JG Prendergast, CA Semple, "Widespread signatures of recent selection linked to nucleosome positioning in the human lineage." Genome Res, (2011) . [offcampus]

10/31: Network Archaeology -- Michael; Felsenstein

11/07: miRNA targets in repetitive coding sequence -- Sam; Tompa

11/14: Gibbs sampling for RNA prediction -- Ajit; Ruzzo

11/21: The role of epistasis in protein and viral evolution -- Dr. Jesse Bloom, FHCRC

11/28: More on nucleosome positioning -- Max; Noble
One or both of

  • A Tsankov, Y Yanagisawa, N Rhind, A Regev, OJ Rando, "Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization." Genome Res, (2011) . [offcampus]
  • JB Zaugg, NM Luscombe, "A genomic model of condition-specific nucleosome behaviour explains transcriptional activity in yeast." Genome Res, (2011) . [offcampus]

12/05: Simplicity in metabolic networks -- John; Borenstein

 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, 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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Seattle, WA  98195-2350
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