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 CSE 590 C, Wi '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, EE1 054
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 Papers
01/09---- Organizational Meeting ----
01/23Adrienne, Jenny; TompaPhyloGibbsPaper
01/30Imran, Luca; NobleProtein phosphorylation motifs from MS dataPaper
02/06Joe Bockhorst, Microsoft ResearchMachine Learning Methods for Discovery of Regulatory Elements in BacteriaAbstract
02/13Jonathan, Nan; FelsensteinStatistical Analysis of Spatially Clustered GenesPaper
02/27Elizabeth, Kasia; RuzzoPost-transcriptional Regulation, IPapers
03/06James, Rosalia, Zizhen; RuzzoPost-transcriptional Regulation, IIPapers

 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.  

01/09: ---- Organizational Meeting ----

01/16: Holiday

01/23: PhyloGibbs -- Adrienne, Jenny; Tompa

01/30: Protein phosphorylation motifs from MS data -- Imran, Luca; Noble

02/06: Machine Learning Methods for Discovery of Regulatory Elements in Bacteria -- Joe Bockhorst, Microsoft Research

   Abstract:   I will present novel machine learning methods for the discovery of important DNA sequence elements encoded in bacterial genomes. Knowledge of these elements provides insight into important problems in computational biology such as uncovering gene functions, gene-regulatory networks, and evolutionary relationships among genes and organisms. This talk will focus on the design and learning of graphical probability models of these elements. I will describe models that incorporate multiple and diverse evidence sources, and methods for modeling and predicting arbitrarily overlapping elements in sequence data. The results of cross-validation experiments on the heavily studied bacterium E. coli show that the accuracy of our predictions exceeds the previous state-of-the-art.

Background Reading:

02/13: Statistical Analysis of Spatially Clustered Genes -- Jonathan, Nan; Felsenstein

02/20: Holiday

02/27: Post-transcriptional Regulation, I -- Elizabeth, Kasia; Ruzzo

   There is considerable evidence in eukaryotes, at least, that mRNAs, once transcribed, are not simply turned loose to diffuse around at random---they are actively transported to specific targets, some being translated, others degraded, others sequestered until needed, etc. Sequence and/or structure motifs in the mRNAs themselves presumably are integral to this control. This week we will look at two articles surveying the current state of knowledge of these processes, and some of the biotechnology used to investigate them. Next week we'll continue by looking at one or more computational papers that attempt to identify relevant motifs in mRNA UTRs.

03/06: Post-transcriptional Regulation, II -- James, Rosalia, Zizhen; Ruzzo

  • Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M., Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals, Nature. 2005 Mar 17;434(7031):338-45 [offcampus]
  • Gerber AP, Herschlag D, Brown PO., Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast., PLoS Biol. 2004 Mar;2(3):E79. [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, 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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