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  CSE 590CAu '15:  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, EE1 031
Organizers: Joe Felsenstein, Sreeram Kannan, Su-In Lee, Bill Noble, Larry Ruzzo, Cole Trapnell
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
10/05---- Organizational Meeting ----
10/12Nikolai; FelsensteinProtein Evolution & DynamicsDetails
10/19Jack & Jacob; NobleChromatin StructureDetails
10/26Max & Alex; NobleMetabolome MS/MSDetails
11/02Scott; HaynorPrediXcanDetails
11/09Katie & Nao; RuzzoNoncoding RNA EvolutionDetails
11/16Safiye; LeePredicting Drug ResponseDetails
11/23Daniel; RuzzoHuman/Mouse Co-Expression(?)Details
11/30Sven & Rahul; LeeRegulation in CancerDetails
12/07Shunfu; KannanSingle-Cell ExpressionDetails
 Papers, etc.

  Note on Electronic Access to Journals

The UW Library is generally a paid subscriber to non-open-access journals we cite. You can freely access these articles from on-campus computers. 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.  

10/05:   -- ---- Organizational Meeting ----

10/12: Protein Evolution & Dynamics -- Nikolai; Felsenstein

10/19: Chromatin Structure -- Jack & Jacob; Noble

10/26: Metabolome MS/MS -- Max & Alex; Noble

  • H Tsugawa, T Cajka, T Kind, Y Ma, B Higgins, K Ikeda, M Kanazawa, J VanderGheynst, O Fiehn, M Arita, "MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis." Nat. Methods, 12, #6 (2015) 523-6. [offcampus]

11/02: PrediXcan -- Scott; Haynor

  • ER Gamazon, HE Wheeler, KP Shah, SV Mozaffari, K Aquino-Michaels, RJ Carroll, AE Eyler, JC Denny, GTEx Consortium, DL Nicolae, NJ Cox, HK Im, "A gene-based association method for mapping traits using reference transcriptome data." Nat. Genet., 47, #9 (2015) 1091-8. [offcampus]

11/09: Noncoding RNA Evolution -- Katie & Nao; Ruzzo

  • A Necsulea, M Soumillon, M Warnefors, A Liechti, T Daish, U Zeller, JC Baker, F Gr├╝tzner, H Kaessmann, "The evolution of lncRNA repertoires and expression patterns in tetrapods." Nature, 505, #7485 (2014) 635-40. [offcampus]
  • H Hezroni, D Koppstein, MG Schwartz, A Avrutin, DP Bartel, I Ulitsky, "Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species." Cell Rep, 11, #7 (2015) 1110-22. [offcampus]

11/16: Predicting Drug Response -- Safiye; Lee

11/23: Human/Mouse Co-Expression(?) -- Daniel; Ruzzo

11/30: Regulation in Cancer -- Sven & Rahul; Lee

12/07: Single-Cell Expression -- Shunfu; Kannan

 Other Seminars Past quarters of CSE 590C
COMBI & Genome Sciences Seminars
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 comprehensive FAQ at, including annotated links to online tutorials and lectures.
CSE 527: Computational Biology
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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