CSE 590 C, Au '05: 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 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.
Email		cse590cb@cs.washington.edu Course-related announcements and discussions   Manage Your Subscription List Archives compbio-seminars@cs.washington.edu Biology seminar announcements from all around campus   Manage Your Subscription List Archives compbio-group@cs.washington.edu Discussions about computational biology   Manage Your Subscription List Archives
Schedule		Date  Presenters/Participants Topic Papers 10/03   ---- Organizational Meeting ----   10/10 Zizhen; Larry Cyanobacterial ncRNA Papers 10/17 John; Larry ncRNA Evolution Papers 10/24 Ilya Shmulevich, ISB Modeling Genetic Networks with Probabilistic Boolean Networks Papers 10/31 James, Imran; Martin De novo repeat detection Papers 11/07 Elizabeth; Bill Motif Discovery Papers 11/14 Alex, Jonathan; Joe Tropical Geometry Papers 11/21 Alex, Jonathan; Joe Tropical Geometry Papers 11/28 Amol; Bill Regulatory Modules Papers 12/05 Rosalia, Adrienne; Martin Phylogenetic Shadowing Papers
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.   10/03: ---- Organizational Meeting ---- --   10/10: Cyanobacterial ncRNA -- Zizhen; Larry Axmann IM, Kensche P, Vogel J, Kohl S, Herzel H, Hess WR, Identification of cyanobacterial non-coding RNAs by comparative genome analysis, Genome Biol. 2005;6(9):R73. Epub 2005 Aug 17 [offcampus] 10/17: ncRNA Evolution -- John; Larry There are several recent papers on this topic; we'll focus on the first one below. Holmes I., A probabilistic model for the evolution of RNA structure, BMC Bioinformatics. 2004 Oct 26;5:166 [offcampus] Holmes I., Accelerated probabilistic inference of RNA structure evolution, BMC Bioinformatics. 2005 Mar 24;6(1):73 [offcampus] Holmes I., Using evolutionary Expectation Maximization to estimate indel rates, Bioinformatics. 2005 May 15;21(10):2294-300. Epub 2005 Feb 24 [offcampus] Rivas E., Evolutionary models for insertions and deletions in a probabilistic modeling framework, BMC Bioinformatics. 2005 Mar 21;6(1):63. [offcampus] 10/24: Modeling Genetic Networks with Probabilistic Boolean Networks -- Ilya Shmulevich, ISB The PBN Web Site [offcampus] 10/31: De novo repeat detection -- James, Imran; Martin Alkes L. Price, Neil C. Jones, Pavel A. Pevzner, De novo identification of repeat families in large genomes, Bioinformatics 21(suppl_1):i351-i358, 2005 [offcampus] 11/07: Motif Discovery -- Elizabeth; Bill Jason Gertz, Linda Riles, Peter Turnbaugh, Su-Wen Ho and Barak A. Cohen, Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics, Genome Research 15:1145-1152, 2005 [offcampus] 11/14: Tropical Geometry -- Alex, Jonathan; Joe Lior Pachter and Bernd Sturmfels, eds., Algebraic Statistics for Computational Biology, Cambridge University Press, to appear. [offcampus] Lior Pachter and Bernd Sturmfels , Tropical geometry of statistical models, PNAS, November 16, 2004, vol. 101, no. 46, 16132-16137 [offcampus] 11/21: Tropical Geometry -- Alex, Jonathan; Joe Ditto. 11/28: Regulatory Modules -- Amol; Bill David C. King, James Taylor, Laura Elnitski, Francesca Chiaromonte, Webb Miller and Ross C. Hardison, Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences, Genome Research 15:1051-1060, 2005 [offcampus] 12/05: Phylogenetic Shadowing -- Rosalia, Adrienne; Martin Dario Boffelli, Jon McAuliffe, Dmitriy Ovcharenko, Keith D. Lewis, Ivan Ovcharenko, Lior Pachter, Edward M. Rubin, Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome, Science, Vol 299, Issue 5611, 1391-1394, 28 February 2003 [offcampus] Dario Boffelli, Marcelo A. Nobrega, Edward M. Rubin, Comparative genomics at the vertebrate extremes, Nature Reviews Genetics 5, 456-465, 2004 [offcampus]
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 bioinformatics.org, 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

	Computer Science & Engineering University of Washington Box 352350 Seattle, WA  98195-2350 (206) 543-1695 voice, (206) 543-2969 FAX [comments to cse590c-webmaster@cs.washington.edu]