image University of Washington Computer Science & Engineering
  CSE 527Au '07:  Computational Biology
  CSE Home   About Us    Search    Contact Info 

Administrative
 Syllabus
 Schedule & Reading
Course Email
 Class List Archive
Assignments
 HW #1
 HW #2
 HW #3
 HW #4
 HW #5
Project Information
 Project Description
 Project Presentations/Reports
Lecture Slides
 1  : Introduction; Bio Basics (1-up4-up)
 2-3: Alignment; DNA Replication (1-up4-up)
 4-5: BLAST, Scoring; Sequencing (1-up4-up)
 6-7: MLE & EM; Gene Expression (1-up4-up)
         EM Example (.xls)
 8-9: Motifs; Gene Regulation (1-up4-up)
 12-13: HMMs (1-up4-up)
 15-16: Genes & Splicing (1-up4-up)
 17-18: RNA Folding; RNA Function (1-up4-up)
 18-20: RNA Motifs, Discovery, & Search (1-up4-up)
Lecture Notes
 0. (All of last year's notes)
 1. Overview
 2. More Bio Overview
 3. Global Alignment
 4. Local Alignment; BLAST
 5. Blast Statistics
 6. DNA Replication; MLE
 7. MLE & EM
 8. TF Binding; Weight Matrices
 9. MEME
 15. Pfam; Genes & Splicing
 16. More Gene Finding
 17. RNA Roles & Structure
 19. CMs II: Search
 20. CMs III: CMfinder
Resources
 Pubmed
 BLAST
 PDB
 NCBI Science Primer
 NHGRI Talking Glossary
 ORNL Genome Glossary
 A Molecular Biology Glossary
   

Lecture:  EEB 026 (schematic) MW 12:00- 1:20 
 
Office Hours Phone
Instructor:  Larry Ruzzo, ruzzo at cs  F 12:00- 1:00  CSE 554  (206) 543-6298

Course Email: cse527a_au07@u.washington.edu. Use this list to ask and/or answer questions about homework, lectures, etc. The instructor and TA are subscribed to this list. All messages are automatically archived.  Questions not of general interest may be directed to the instructor: ruzzo at cs. You can (and perhaps should) change your subscription options.

Catalog 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. Prerequisite: graduate standing in biological, computer, mathematical or statistical science, or permission of instructor.

Prerequisite: None.

Credits: 3

Textbook: Richard Durbin, Sean R. Eddy, Anders Krogh and Graeme Mitchison, Biological Sequence Analysis: Probabilistic models of proteins and nucleic acids, Cambridge, 1998. (U. Book Store, Amazon) Errata.

References: See Schedule & Reading.


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: © 1993-2007, Department of Computer Science and Engineering, University of Washington.

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