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  CSE 590CAu '06:  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 042
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
10/02---- Organizational Meeting ----
10/09Elizabeth T; TompaThe Microbial Pan-GenomeDetails
10/16Dan B, Adrienne W; TompaNucleosome PositioningDetails
10/23James T, Pascal C; NobleNetwork Multiple AlignmentDetails
10/30Dan H; FelsensteinFast multiple sequence alignment?Details
11/06Becky D, Kasia W; RuzzoAn RNA Gene in Human BrainDetails
11/13Zizhen Y, Elaine C; NobleSampling Protein ConformationsDetails
11/20Nguyen N, Imran R; RuzzoRNA 2ary Structure & Sequence MotifsDetails
11/27Cristina G, Jonathan C; FelsensteinComparative Exon DetectionDetails
12/04Arturo Centurion, UW Dept. of MedicineGene Regulation in T. pallidum 

 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.  

10/02: ---- Organizational Meeting ----

10/09: The Microbial Pan-Genome -- Elizabeth T; Tompa

  • H Tettelin, V Masignani, MJ Cieslewicz, C Donati, D Medini, NL Ward, SV Angiuoli, J Crabtree, AL Jones, AS Durkin, RT Deboy, TM Davidsen, M Mora, M Scarselli, I Margarit y Ros, JD Peterson, CR Hauser, JP Sundaram, WC Nelson, R Madupu, LM Brinkac, RJ Dodson, MJ Rosovitz, SA Sullivan, SC Daugherty, DH Haft, J Selengut, ML Gwinn, L Zhou, N Zafar, H Khouri, D Radune, G Dimitrov, K Watkins, KJ O'Connor, S Smith, TR Utterback, O White, CE Rubens, G Grandi, LC Madoff, DL Kasper, JL Telford, MR Wessels, R Rappuoli, CM Fraser, "Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"." Proc. Natl. Acad. Sci. U.S.A., 102, #39 (2005) 13950-5. [offcampus]

10/16: Nucleosome Positioning -- Dan B, Adrienne W; Tompa

10/23: Network Multiple Alignment -- James T, Pascal C; Noble

10/30: Fast multiple sequence alignment? -- Dan H; Felsenstein

11/06: An RNA Gene in Human Brain -- Becky D, Kasia W; Ruzzo

  • KS Pollard, SR Salama, N Lambert, MA Lambot, S Coppens, JS Pedersen, S Katzman, B King, C Onodera, A Siepel, AD Kern, C Dehay, H Igel, M Ares, P Vanderhaeghen, D Haussler, "An RNA gene expressed during cortical development evolved rapidly in humans." Nature, 443, #7108 (2006) 167-72. [offcampus]
Their companion paper
  • KS Pollard, SR Salama, B King, AD Kern, T Dreszer, S Katzman, A Siepel, JS Pedersen, G Bejerano, R Baertsch, KR Rosenbloom, J Kent, D Haussler, "Forces Shaping the Fastest Evolving Regions in the Human Genome." PLoS Genet, 2, #10 (2006) . [offcampus]
has more details about methods and general discussion of the other accelerated regions found.

11/13: Sampling Protein Conformations -- Zizhen Y, Elaine C; Noble

11/20: RNA 2ary Structure & Sequence Motifs -- Nguyen N, Imran R; Ruzzo

11/27: Comparative Exon Detection -- Cristina G, Jonathan C; Felsenstein

12/04: Gene Regulation in T. pallidum -- Arturo Centurion, UW Dept. of Medicine

 Other  Seminars Past quarters of CSE 590C
COMBI & Genome Sciences Seminars
Applied Math Department Mathematical Biology Journal Club
Biostatistics Seminars
Microbiology Department Seminars
Zoology 525, Mathematical Biology Seminar Series

 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.
S-Star Bioinformatics Online Course Schedule, a collection of video primers
A very comprehensive FAQ at, including annotated references to online tutorials and lectures.
CSE 527: Computational Biology
CSE 590TV: 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
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