CSE 590 CB, Au '04: Reading & Research in Comp. Bio.

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Course Info		CSE 590CB 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, MEB 243 Organizers:  Joe Felsenstein, Michal Linial, Bill Noble, Emily Rocke, 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 10/04   ---- Organizational Meeting ----   10/11 Ka Yee Yeung, Microbiology and CEA Gene selection using Bayesian Model Averaging: application to multi-class classification of microarray data Abstract 10/18 Jonathon, Travis (Emily) Position-based Motif Discovery Paper 10/25 Alex, Ross (Martin) Mammal Sequencing: Who's next? Paper 11/01 Brig, Zasha (Larry) Finding ncRNA Genes Paper 11/08 Ora Furman, Biochemistry Docking   11/15 Divya, Kasia, Nan, Rosalia (Michal) Detecting Signatures in Proteins Papers 11/22 Divya, Kasia, Nan, Rosalia (Michal) Integration of Biological Data Papers 11/29 Greg, Lisa, Zizhen (Joe) Expression to Phylogeny Papers 12/06 Amol, Becky (Bill) Quality Assessment of Tandem Mass Spectra 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, look at the library "proxy server" instructions. During Autumn 2004, the Library is deploying a new proxy server; if you are accessing this page from an offcampus computer, the "[offcampus]" links below may be more convenient. You will be prompted for your UW net ID and password once per session.   10/11: Gene selection using Bayesian Model Averaging: application to multi-class classification of microarray data -- Ka Yee Yeung, Microbiology and CEA     Abstract:  Motivation: Selection of relevant genes is critical to accurately predict the class of a tissue sample from its gene expression profiles. In this talk, we present the merits of using Bayesian Model Averaging (BMA) in gene selection and classification on microarray data. Typical gene selection and classification procedures ignore model uncertainty such that one set of relevant genes (model) is chosen to predict the class. BMA accounts for the model uncertainty by averaging over multiple models (sets of potentially overlapping relevant genes). Results: We showed that BMA selects relatively small numbers of relevant genes and achieves high prediction accuracy on three microarray datasets. Our BMA algorithm is applicable to microarray datasets with any numbers of classes, outputs posterior probabilities for the selected genes and models. Our selected models are typically simple, consisting of only a few genes. By averaging over multiple simple models, our BMA algorithm achieves high prediction accuracy. 10/18: Position-based Motif Discovery -- Jonathon, Travis (Emily) Peter C. FitzGerald, Andrey Shlyakhtenko, Alain Mir, and Charles Vinson, Clustering of DNA Sequences in Human Promoters, Genome Research 14:1562-1574 [offcampus] 10/25: Mammal Sequencing: Who's next? -- Alex, Ross (Martin) Gregory M. Cooper et al., Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes, Genome Research, Vol 13, Issue 5, 813-820, May 2003 [offcampus] 11/01: Finding ncRNA Genes -- Brig, Zasha (Larry) Coventry A, Kleitman DJ, Berger B., MSARI: multiple sequence alignments for statistical detection of RNA secondary structure, Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12102-7. Epub 2004 Aug 10. [offcampus] 11/08: Docking -- Ora Furman, Biochemistry 11/15: Detecting Signatures in Proteins -- Divya, Kasia, Nan, Rosalia (Michal) Pe'er I, Felder CE, Man O, Silman I, Sussman JL, Beckmann JS, Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla, Proteins 2004 Jan 1 54(1):20-40 [offcampus] Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW,, Weissman JS, O'Shea EK, Global analysis of protein localization in budding yeast, Nature 2003 Oct 16 425(6959):686-91 [offcampus] 11/22: Integration of Biological Data -- Divya, Kasia, Nan, Rosalia (Michal) Hirai MY, Yano M, Goodenowe DB, Kanaya S, Kimura T, Awazuhara M, Arita M, Fujiwara T, Saito K, Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana, Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):10205-10 [offcampus] King RD, Whelan KE, Jones FM, Reiser PG, Bryant CH, Muggleton SH, Kell DB, Oliver SG, Functional genomic hypothesis generation and experimentation by a robot scientist, Nature 2004 Jan 15 427(6971):247-52 [offcampus] 11/29: Expression to Phylogeny -- Greg, Lisa, Zizhen (Joe) Uddin M, Wildman DE, Liu G, Xu W, Johnson RM, Hof PR, Kapatos G, Grossman LI, and Goodman M., Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles., Proc Natl Acad Sci USA. 2004 Mar 2;101(9):2957-62 [offcampus] Gu X., Statistical framework for phylogenomic analysis of gene family expression profiles, Genetics. 2004 May;167(1):531-42 [offcampus] 12/06: Quality Assessment of Tandem Mass Spectra -- Amol, Becky (Bill) Marshall Bern, David Goldberg, W. Hayes McDonald and John R. Yates, III, Automatic Quality Assessment of Peptide Tandem Mass Spectra, Bioinformatics 20(Suppl. 1) 2004, i49-i54 [offcampus] Tomasz Bczek, Adam Buciski, Alexander R. Ivanov, and Roman Kaliszan, Artificial Neural Network Analysis for Evaluation of Peptide MS/MS Spectra in Proteomics, Anal. Chem., 76 (6), 1726 -1732, 2004. 10.1021/ac030297u S0003-2700(03)00297-X [offcampus]
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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