Retro prof-type at desk University of Washington Department of Computer Science & Engineering
 CSE 527: Computational Biology
  CSE Home   About Us    Search    Contact Info 

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: 01/11/02, 07PM.)
   To subscribe to the mailing list: click here, then fill in your email address and send. Or send email to 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:

  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

Portions of the CSE 527 Web may be reprinted or adapted for academic nonprofit purposes, providing the source is accurately quoted and duly credited. The CSE 527 Web: © 1993-2001, Department of Computer Science and Engineering, University of Washington.

CSE logo Department of Computer Science & Engineering
University of Washington
Box 352350
Seattle, WA  98195-2350
(206) 543-1695 voice, (206) 543-2969 FAX
[comments to webmaster]