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  CSE 590CWi '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, MGH 284 (schematic)
Organizers:  Joe Felsenstein, 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
01/07---- Organizational Meeting ----
01/14Maxim, Philip; Felsenstein"Data cloning" for MCMCDetails
01/28Patricio, Emilia; RuzzoBirth and Evolution of Mammalian miRNAsDetails
02/04Max, Sonya; NobleEpigenome DynamicsDetails
02/11Aaron; NobleDNA-DNA contact mappingDetails
02/25Peter, Jeremy; TompaAncient SyntenyDetails
03/04Alex; TompaTime-series MetagenomicsDetails
03/11Daniel, Safiye; FelsensteinDirichlet MixturesDetails

 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.  

01/07: ---- Organizational Meeting ----

01/14: "Data cloning" for MCMC -- Maxim, Philip; Felsenstein


01/21:   -- Holiday

01/28: Birth and Evolution of Mammalian miRNAs -- Patricio, Emilia; Ruzzo

02/04: Epigenome Dynamics -- Max, Sonya; Noble

  • P Arnold, A Schöler, M Pachkov, PJ Balwierz, H Jørgensen, MB Stadler, E van Nimwegen, D Schübeler, "Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting." Genome Res., 23, #1 (2013) 60-73. [offcampus]

02/11: DNA-DNA contact mapping -- Aaron; Noble

02/18:   -- Holiday

02/25: Ancient Synteny -- Peter, Jeremy; Tompa

  • M Irimia, JJ Tena, MS Alexis, A Fernandez-Miñan, I Maeso, O Bogdanovic, E de la Calle-Mustienes, SW Roy, JL Gómez-Skarmeta, HB Fraser, "Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints." Genome Res., 22, #12 (2012) 2356-67. [offcampus]

03/04: Time-series Metagenomics -- Alex; Tompa

  • I Sharon, MJ Morowitz, BC Thomas, EK Costello, DA Relman, JF Banfield, "Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization." Genome Res., 23, #1 (2013) 111-20. [offcampus]

03/11: Dirichlet Mixtures -- Daniel, Safiye; 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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Seattle, WA  98195-2350
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