CSE Comp Bio group logo University of Washington Department of Computer Science & Engineering
 CSE 590 CB, Winter 2004
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Reading and Research in Computational Biology
Mondays, 3:30 - 4:50, EE1 026

CSE 590CB is a weekly seminar on Readings and Research in Computational Biology, open to all graduate students in the computer, biological, and mathematical sciences.
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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 Schedule
Date Presenters/Participants Topic Papers
01/05   Organizational meeting  
01/12 Cherniavsky, Felsenstein Genetic Algorithms For Searching Phylogeny Space Papers
01/19   Martin Luther King Day  
01/26 Gehlenborg, Wilamowska, Ruzzo, Tompa RNA Sensors and Riboswitches Papers
02/02 Ringenburg, Yao, Ruzzo, Tompa Finding Structure Motifs in a Set of RNA Sequences Paper
02/09 Hoffmann, Lambert, Noble Splicing Identified by Support Vector Machines Paper
02/16   Presidents Day  
02/23 Weinberg, Ruzzo, Tompa ncRNA Detection By Comparative Sequence Analysis Paper
03/01 Prakash, Felsenstein "Ratcheting" Phylogenies Papers
03/08 Li, Noble Phylogenetic Data and Co-regulated Genes to Identify Regulatory Motifs Paper

 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, look at the library "proxy server" instructions.  


01/12: Genetic algorithms for searching phylogeny space

  • Lewis, P. O. 1998. A genetic algorithm for maximum-likelihood phylogeny using nucleotide sequence data. Molecular Biology and Evolution 15: 277-283.
  • Matsuda, H. 1996. Protein phylogenetic inference using maximum likelihood with a genetic algorithm. Pacific Symposium on Biocomputing 1996, pp. 512--523. (no link available)
  • Moilanen, A. 1999. Searching for most parsimonious trees with simulated evolutionary optimization. Cladistics 15: 39-50. (I couldn't get a link to paste in that works, but is available in UW e-journals)
  • Katoh, K., K. Kuma, and T. Miyata. 2001. Genetic algorithm-based maximum-likelihood analysis for molecular phylogeny. Journal of Molecular Evolution 53: 477-484.
  • Congdon, C. B. 2001. Gaphyl: A genetic algorithms approach to cladistics. pp. 67--78 in "Principles of Data Mining and Knowledge Discovery", ed. L. DeRaedt and A. Siebes. Lecture Notes in Computer Science, No. 2168. Springer-Verlag, Berlin. (no link available)

01/26: RNA Sensors and Riboswitches

First three articles below are reviews; last ones are more technical.
  • Narasimhan Sudarsan, Jeffrey E. Barrick And Ronald R. Breaker, Metabolite-binding RNA domains are present in the genes of eukaryotes, RNA (2003), 9:644-647
  • Maumita Mandal, Benjamin Boese, Jeffrey E. Barrick, Wade C. Winkler, and Ronald R. Breaker, Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria, Cell, Vol 113, 577-586, 30 May 2003

02/02: Finding Structure Motifs in a Set of RNA Sequences

02/09: Splicing Identified by Support Vector Machines

  • Xiang H-F. Zhang, Katherine A. Heller, Ilana Hefter, Christina S. Leslie and Lawrence A. Chasin, Sequence Information for the Splicing of Human Pre-mRNA Identified by Support Vector Machine Classification, Genome Research 13:2637-2650, 2003

02/23: ncRNAs Detection by Comparative Sequence Analysis

03/01: "Ratcheting" Phylogenies

03/08: Phylogenetic Data and Co-regulated Genes to Identify Regulatory Motifs


 Other  Seminars Past quarters of CSE 590CB
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


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University of Washington
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Seattle, WA  98195-2350
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