CSE 527: Computational Biology

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Current Quarter  2001 Autumn (Ruzzo) Previous Quarters  2000 Winter (Tompa)  1998 Winter (Karp, Ruzzo)  1996 Winter (Karp, Ruzzo, Tompa)

Description: Introduces computational methods for understanding biological systems at the molecular level. Problem areas such as mapping and sequencing, sequence analysis, structure prediction, phylogenic inference, regulatory analysis. Techniques such as dynamic programming, Markov models, expectation-maximization, local search. Was offered as CSE 590BI in earlier years. Prerequisites: Prerequisites: graduate standing in biological, computer, mathematical or statistical science, or permission of instructor. Credits: 3 Email: Email Log (All mail sent to cse527@cs. Last: .)    To subscribe to the mailing list: click here, then fill in your email address and send. Or send email to majordomo@cs.washington.edu with "subscribe cse527" as the body (not subject) of the message. Either way, you will get an automatic reply from majordomo; follow the directions in this message to complete your subscription. Lecture Notes: (10/02/01): Intro: excerpts from GEN 220 lecture slides (PowerPoint), Dr. Holly Dressman, Duke Genome Core Facility (10/04/01): Microarrays (Peter Mork) (10/09/01): Comparison of Microarray Technologies (Simon Kahan) (10/16/01): Applications of Microarrays (Brian Tjaden) (10/18/01): Clustering (Tobias Mann) (10/23/01): Hierarchical clustering (Shabnam Erfani) (10/25/01): Graph theory, cliques (Daniel Grossman)(PS version) (10/30/01): More Clustering (Peter Couperus)(PS version) (11/01/01): Model based clustering (Shabnam Erfani)  Model based clustering of gene expression (Power Point show)   (html version) (11/06/01): EM clustering (Tushar Bhangale) (PDF version) (11/08/01): EM continued (Kai Wang) (11/13/01): Motif finding (Scott Votaw; PS version) (PDF version) (11/20/01): Bayesian Model Selection (Daehyun Baek) (PDF version) (11/20/01): Viterbi algo (Zizhen Yao) (12/04/01): Viterbi algo cotinued (William Pentney; PS version) (PDF version) (12/04/01): Gene Prediction (Tobias Mann) (12/06/01): Gene Prediction (Hao Mei) (12/11/01): Gene Finding (Peter Couperus; PS version) (PDF version) Useful links: GeneX analysis and database server (local) Seminars and classes at the UW Computational molecular biology at the UW and FHCRC Applied Math Department Mathematical Biology Journal Club Biochemistry Department Seminars COMBI Seminars (MBT 551) Genetics Department Seminars Microbiology Department Seminars Molecular Biotechnology Department Seminars Zoology 525, Mathematical Biology Seminar Series MBT 599 (aka MBT/GENET 540/541) Introduction to Computational Molecular Biology: Genome and Protein Sequence Analysis (Winter/Spring 2001) Quicktime Movies: Some nice animation/movies. Let me know if you find others. DNA model: http://www.mediaspin.com/dna.html DNA replication: http://academy.d20.co.edu/kadets/lundberg/DNA_animations/DNAreplication.mov Mitosis in Arabidopsis: http://academy.d20.co.edu/kadets/lundberg/DNA_animations/aavideo.mov Biological background information and animations Eukaryotic Transcription http://www.mun.ca/biochem/courses/3107/Lectures/Topics/euk_transcription.html Microbial Genetics and Microbial Metabolism http://www.cat.cc.md.us/courses/bio141/lecguide/unit4/u4ib5.html Johnson Explorations (Shockwave required) http://www.mhhe.com/biosci/genbio/biolink/j_explorations/explorations.html Molecular Image http://www.ircm.qc.ca/benoitcoulombe/A-ModelisationMoleculaire1.html Molecular Biology (Shockwave required) http://www.lsic.ucla.edu/ls3/tutorials/gene_expression.html Several animation in transcriptional regulation (The RNA Polymerase-Attenuation Project) http://berget.mcs.cmu.edu/WWWRNAP/RNAPprojectOverview.html

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