Retro prof-type at desk University of Washington Department of Computer Science & Engineering
 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

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Lecture Notes:

  1. (10/02/01): Intro: excerpts from GEN 220 lecture slides (PowerPoint), Dr. Holly Dressman, Duke Genome Core Facility
  2. (10/04/01): Microarrays (Peter Mork)
  3. (10/09/01): Comparison of Microarray Technologies (Simon Kahan)
  4. (10/16/01): Applications of Microarrays (Brian Tjaden)
  5. (10/18/01): Clustering (Tobias Mann)
  6. (10/23/01): Hierarchical clustering (Shabnam Erfani)
  7. (10/25/01): Graph theory, cliques (Daniel Grossman)(PS version)
  8. (10/30/01): More Clustering (Peter Couperus)(PS version)
  9. (11/01/01): Model based clustering (Shabnam Erfani)  Model based clustering of gene expression (Power Point show)   (html version)
  10. (11/06/01): EM clustering (Tushar Bhangale) (PDF version)
  11. (11/08/01): EM continued (Kai Wang)
  12. (11/13/01): Motif finding (Scott Votaw; PS version) (PDF version)
  13. (11/20/01): Bayesian Model Selection (Daehyun Baek) (PDF version)
  14. (11/20/01): Viterbi algo (Zizhen Yao)
  15. (12/04/01): Viterbi algo cotinued (William Pentney; PS version) (PDF version)
  16. (12/04/01): Gene Prediction (Tobias Mann)
  17. (12/06/01): Gene Prediction (Hao Mei)
  18. (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

Quicktime Movies: Some nice animation/movies. Let me know if you find others. Biological background information and animations


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