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  CSE 590CWi '14:  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 045 (schematic)
Organizers:  Joe Felsenstein, Su-In Lee, Bill Noble, Larry Ruzzo
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
01/06---- Organizational Meeting ----
01/13Daniel; LarryPeer reviewDetails
01/27Scott; LarryIn vivo RNA structureDetails
02/03Maxim; JoeEvolution of RobustnessDetails
02/10Safiye; JoeEvolution of Regulation from Transcriptional ProfilesDetails
02/24Max; BillQuality of ChIP-seq DataDetails
03/03Patricio; Su-InFunctional variants in cancer genomesDetails
03/10Alex; BillQuantifying Coeluting PeptidesDetails

 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.  

01/06: ---- Organizational Meeting ----

01/13: Peer review -- Daniel; Larry

    Everyone should read the article below: plus one or two others on the peer review process, such as the ones listed here: or find others via Google or PubMed. ``Peer Review,'' ``Flaws,'' and ``Pit Bulls'' are likely search terms, (but no man-bites-dog stories, please). The goal is to have a discussion about this, rather than the usual one-sided presentation, and it will be much more interesting if we bring a diversity of opinions.

01/20:   -- Holiday

01/27: In vivo RNA structure -- Scott; Larry

  • S Rouskin, M Zubradt, S Washietl, M Kellis, JS Weissman, "Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo." Nature, (2013) . [offcampus]

02/03: Evolution of Robustness -- Maxim; Joe

02/10: Evolution of Regulation from Transcriptional Profiles -- Safiye; Joe

02/17:   -- Holiday

02/24: Quality of ChIP-seq Data -- Max; Bill

03/03: Functional variants in cancer genomes -- Patricio; Su-In

  • A Gonzalez-Perez, V Mustonen, B Reva, GR Ritchie, P Creixell, R Karchin, M Vazquez, JL Fink, KS Kassahn, JV Pearson, GD Bader, PC Boutros, L Muthuswamy, BF Ouellette, J Reimand, et 14 al., "Computational approaches to identify functional genetic variants in cancer genomes." Nat. Methods, 10, #8 (2013) 723-9. [offcampus]

03/10: Quantifying Coeluting Peptides -- Alex; Bill

  • P Schliekelman, S Liu, "Quantifying the Effect of Competition for Detection between Coeluting Peptides on Detection Probabilities in Mass-Spectrometry-Based Proteomics." J. Proteome Res., (2013) . [offcampus]

 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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