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  CSE 590CAu '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, EEB 031 (schematic)
Organizers:  Joe Felsenstein, Bill Noble, Larry Ruzzo, Harlan Robins
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
10/01---- Organizational Meeting ----
10/08Dr. Lukas Kall, UW Genome SciencesHMM posterior decoding for Transmembrane PredictionDetails
10/15Imran, Elaine (Bill)Protein-Protein InteractionDetails
10/22Zizhen (Joe)Indel Max LikelihoodDetails
10/29Benjamin, Xiaoyu (Bill)TFBS Diversity in YeastDetails
11/05Adrienne (Larry)Selection in ncRNADetails
11/19Elizabeth (Joe)Yggdrasil: sampling sequence motifs from a tree mixture modelDetails
11/26Nguyen, Josh (Harlan)Physical models of protein/DNA interaction from ChIP-chip dataDetails
12/03Yanping, Deepak (Harlan)Information Theory applied to biologyDetails

 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.  

10/01: ---- Organizational Meeting ----

10/08: HMM posterior decoding for Transmembrane Prediction -- Dr. Lukas Kall, UW Genome Sciences

10/15: Protein-Protein Interaction -- Imran, Elaine (Bill)

  • Ramon Aragues, Andrej Sali, Jaume Bonet, Marc A. Marti-Renom, Baldo Oliva, "Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions," PLoS Comput Biol, 3, #9 (2007) e178.

10/22: Indel Max Likelihood -- Zizhen (Joe)

10/29: TFBS Diversity in Yeast -- Benjamin, Xiaoyu (Bill)

  • AR Borneman, TA Gianoulis, ZD Zhang, H Yu, J Rozowsky, MR Seringhaus, LY Wang, M Gerstein, M Snyder, "Divergence of transcription factor binding sites across related yeast species." Science, 317, #5839 (2007) 815-9. [offcampus]

11/05: Selection in ncRNA -- Adrienne (Larry)

11/12:   -- Holiday

11/19: Yggdrasil: sampling sequence motifs from a tree mixture model -- Elizabeth (Joe)

11/26: Physical models of protein/DNA interaction from ChIP-chip data -- Nguyen, Josh (Harlan)

12/03: Information Theory applied to biology -- Yanping, Deepak (Harlan)

 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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Seattle, WA  98195-2350
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