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.
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 01/09 ---- Organizational Meeting ---- 01/16 Holiday 01/23 Adrienne, Jenny; Tompa PhyloGibbs Paper 01/30 Imran, Luca; Noble Protein phosphorylation motifs from MS data Paper 02/06 Joe Bockhorst, Microsoft Research Machine Learning Methods for Discovery of Regulatory Elements in Bacteria Abstract 02/13 Jonathan, Nan; Felsenstein Statistical Analysis of Spatially Clustered Genes Paper 02/20 Holiday 02/27 Elizabeth, Kasia; Ruzzo Post-transcriptional Regulation, I Papers 03/06 James, Rosalia, Zizhen; Ruzzo Post-transcriptional Regulation, II 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.   01/09: ---- Organizational Meeting ---- 01/16: Holiday 01/23: PhyloGibbs -- Adrienne, Jenny; Tompa Siddharthan R, Siggia ED, van Nimwegen E, PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny, PLoS Comput Biol 1(7): e67 [offcampus] 01/30: Protein phosphorylation motifs from MS data -- Imran, Luca; Noble Schwartz D, Gygi SP, An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets, Nat Biotechnol. 2005 Nov;23(11):1391-8. [offcampus] 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: Bockhorst J, Qiu Y, Glasner J, Liu M, Blattner F, Craven M., Predicting bacterial transcription units using sequence and expression data, Bioinformatics. 2003;19 Suppl 1:i34-43. [offcampus] J. Bockhorst and M. Craven, Markov Networks for Detecting Overlapping Elements in Sequence Data, Advances in Neural Information Processing Systems 17 (NIPS 2004). MIT Press [offcampus] 02/13: Statistical Analysis of Spatially Clustered Genes -- Jonathan, Nan; Felsenstein Hoberman R, Sankoff D, Durand D., The statistical analysis of spatially clustered genes under the maximum gap criterion, J Comput Biol. 2005 Oct;12(8):1083-102. [offcampus] 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. Moore MJ., From birth to death: the complex lives of eukaryotic mRNAs, Science. 2005 Sep 2;309(5740):1514-8. [offcampus] Hieronymus H, Silver PA., A systems view of mRNP biology., Genes Dev. 2004 Dec 1;18(23):2845-60. [offcampus] 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] Shalgi R, Lapidot M, Shamir R, Pilpel Y., A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs., Genome Biol. 2005;6(10):R86. [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] Davuluri RV, Suzuki Y, Sugano S, Zhang MQ., CART classification of human 5' UTR sequences., Genome Res. 2000 Nov;10(11):1807-1 [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

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