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  CSE 590CAu '13:  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 025 (schematic)
Organizers:  Hamid Bolouri, Elhanan Borenstein, Joe Felsenstein, 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
09/30---- Organizational Meeting ----
10/07Danielle, John; Bolouri/RuzzoExpression2Kinases Details
10/14Maxim, Sonya; BorensteinNetwork Discovery Details
10/21Patricio; FelsensteinSelective Sweeps Details
10/28Scott; RuzzononcodingRNA Details
11/04Peter; FelsensteinViral Phylodynamics Details
11/18Alex, Daniel; NobleChromatin Conformation Details
11/25Max; BorensteinMetagenomics Details
12/02Mason, Safiye; Bolouri/RuzzoRegulatory Architecture Details

 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.  

09/30: ---- Organizational Meeting ----

10/07: Expression2Kinases -- Danielle, John; Bolouri/Ruzzo

10/14: Network Discovery -- Maxim, Sonya; Borenstein

10/21: Selective Sweeps -- Patricio; Felsenstein

A useful background paper:

10/28: noncodingRNA -- Scott; Ruzzo

11/04: Viral Phylodynamics -- Peter; Felsenstein

11/11:   -- Holiday

11/18: Chromatin Conformation -- Alex, Daniel; Noble

  • T Nagano, Y Lubling, TJ Stevens, S Schoenfelder, E Yaffe, W Dean, ED Laue, A Tanay, P Fraser, "Single-cell Hi-C reveals cell-to-cell variability in chromosome structure." Nature, (2013) . [offcampus]

11/25: Metagenomics -- Max; Borenstein

  • MG Langille, J Zaneveld, JG Caporaso, D McDonald, D Knights, JA Reyes, JC Clemente, DE Burkepile, RL Vega Thurber, R Knight, RG Beiko, C Huttenhower, "Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences." Nat. Biotechnol., 31, #9 (2013) 814-21. [offcampus]

12/02: Regulatory Architecture -- Mason, Safiye; Bolouri/Ruzzo

  • DJ Gaffney, JB Veyrieras, JF Degner, R Pique-Regi, AA Pai, GE Crawford, M Stephens, Y Gilad, JK Pritchard, "Dissecting the regulatory architecture of gene expression QTLs." Genome Biol., 13, #1 (2012) R7. [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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Seattle, WA  98195-2350
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