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 CSE 590 CB, Autumn 2000
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Reading and Research in Computational Biology
Wednesdays, 3:30 - 5:00, 112 Loew

CSE 590 CB is a weekly seminar on Readings and Research in Computational Biology, open to all graduate students in the computer, biological, and mathematical sciences.
Instructors:  Larry Ruzzo, Rimli Sengupta
Credit: 1-3 Variable
Grading: Credit/No Credit. Talk to an instructor if you are unsure of our expectations.
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 Preliminary  Schedule
Date Topic Presenters/Participants Papers
9/27 Overview of local activities  
10/04 Organizational Meeting   
10/11 Motifs Saurabh; Larry Papers
10/18 "The bioinformatics of the Xylella fastidiosa genome project" Joao Carlos Setubal - Instituto de Computacao-UNICAMP Web Site
10/25 "Gene prediction in C. elegans" Phil Green  
11/1 PCA/SVD for Microarrays Emily, Ka Yee, Tammy; Larry Papers
11/8
11/15 Haplotyping Don, Jeremy Papers 
11/22 Motifs & Clustering, I Chris, Jochen, Ken, Matthieu; Rimli, Larry Papers
11/29   Benno  
12/6 Motifs & Clustering, II    

 Papers, etc. : Nature Genetics and maybe some of the other journal links below require a password, which is available to UW students and staff; click here.


10/11:  Motif Finding

We are planning to discuss the following paper, which uses some ideas from statistical physics to do motif finding.

Reference:


11/1 & 11/18:  SVD/PCA & Microarrays

Several groups have independently proposed using Singular Value Decomposition, aka Principal Component Analysis, as part of the analysis of gene expression microarry data. We'll look at what it is and whether it's a good idea.

References:


11/15:  Haplotyping

Humans are diploid, but for many studies, it's more valuable to know haplotypes. We'll look at why, and at a paper proposing an approach to infering haplotypes.

Reference:


11/22 & 12/6:  Motifs and Clustering

For analysis of gene expression data, several groups have proposed clustering, followed by identification of upstream promoter motifs within clusters. A recent proposal is to do both simultaneously.

References:



 Other  Seminars Applied Math Department Mathematical Biology Journal Club
Biochemistry Department Seminars
COMBI Seminars (MBT 599C)
Genetics Department Seminars
Microbiology Department Seminars
Molecular Biotechnology Department Seminars
Zoology 525, Mathematical Biology Seminar Series

 Resources CSE 590 CB, Spring, 2000.
CSE 590 CB, Winter, 2000.
CSE 590 CB, Autumn, 1999.
CSE 590 CB, Spring, 1999.
CSE 590 CB, Winter, 1999.
CSE 590 CB, Autumn, 1998.
Lecture notes from the three offerings of CSE 527 (Computational Biology) (formerly known as CSE 590 BI).


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