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  CSE 590CAu '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 026 (schematic)
Organizers:  Elhanan Borenstein, Joe Felsenstein, Hamid Bolouri, Bill Noble, 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
10/04---- Organizational Meeting ----
10/11Eric, Kris; TompaSelection in the Dog genomeDetails
10/18Brandon; NobleMass Defect FiltersDetails
10/25Eric, Elizabeth; RuzzolincRNADetails
11/01Benjamin; NobleChimeric Mass SpectraDetails
11/08Xiaoyu, Stella; NobleTumorigenesisDetails
11/15Dustin; BolouriChIPseq StatisticsDetails
11/22James; LeePathways from InteractionsDetails
11/29Stella; BorensteinMetagenomicsDetails
12/06Miles, Dustin; Felsensteinvon Neuman rejection samplingDetails

 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.  

10/04: ---- Organizational Meeting ----

10/11: Selection in the Dog genome -- Eric, Kris; Tompa

10/18: Mass Defect Filters -- Brandon; Noble

10/25: lincRNA -- Eric, Elizabeth; Ruzzo

  • M Guttman, I Amit, M Garber, C French, MF Lin, D Feldser, M Huarte, O Zuk, BW Carey, JP Cassady, MN Cabili, R Jaenisch, TS Mikkelsen, T Jacks, N Hacohen, et 5 al., "Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals." Nature, 458, #7235 (2009) 223-7. [offcampus]
  • M Guttman, M Garber, JZ Levin, J Donaghey, J Robinson, X Adiconis, L Fan, MJ Koziol, A Gnirke, C Nusbaum, JL Rinn, ES Lander, A Regev, "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs." Nat. Biotechnol., 28, #5 (2010) 503-10. [offcampus]

11/01: Chimeric Mass Spectra -- Benjamin; Noble

11/08: Tumorigenesis -- Xiaoyu, Stella; Noble

  • E Letouzé, Y Allory, MA Bollet, F Radvanyi, F Guyon, "Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis." Genome Biol., 11, #7 (2010) R76. [offcampus]

11/15: ChIPseq Statistics -- Dustin; Bolouri

  • Unpublished paper by Gottardo, available soon

11/22: Pathways from Interactions -- James; Lee

11/29: Metagenomics -- Stella; Borenstein
Some combination of:

12/06: von Neuman rejection sampling -- Miles, Dustin; Felsenstein

 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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University of Washington
Box 352350
Seattle, WA  98195-2350
(206) 543-1695 voice, (206) 543-2969 FAX