| Course Info |
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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
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| 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
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Web Site |
| 10/25 |
"Gene prediction in C. elegans" |
Phil Green |
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| 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 |
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| 12/6 |
Motifs & Clustering, II |
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| 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:
- S. Raychaudhuri, J.M. Stuart, and R.B. Altman,
Principal Components Analysis to Summarize Microarray
Experiments: Application to Sporulation Time Series
PSB 2000.
- Neal S. Holter, Madhusmita Mitra, Amos Maritan, Marek
Cieplak, Jayanth R. Banavar, and Nina V. Fedoroff
Fundamental patterns underlying gene expression profiles:
Simplicity from complexity
PNAS 97: 8409-8414.
- Orly Alter, Patrick O. Brown, and David Botstein
Singular value decomposition for genome-wide expression data
processing and modeling
PNAS 97: 10101-10106.
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Trevor Hastie, Robert Tibshirani Michael B Eisen, Ash
Alizadeh, Ronald Levy, Louis Staudt, Wing C Chan, David
Botstein, Patrick Brown
'Gene shaving' as a method for identifying distinct sets of
genes with similar expression patterns,
Genome Biology, 2000.
-
M. Bittner, P. Meltzer, Y. Chen, Y. Jiang, E. Seftor, M.
Hendrix, M. Radmacher, R. Simon, Z. Yakhini, et. al,
Molecular classification of cutaneous malignant melanoma
by gene expression profiling
Nature Volume 406 Number 6795 Page 536 - 540 (2000).
[Actually, this paper uses Multi-Dimensional Scaling, a
related technique.]
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:
- Ian Holmes, William J. Bruno,
Finding Regulatory Elements Using Joint Likelihoods for
Sequence and Expression Profile Data
ISMB 2000, 202-210.
- Jaak Vilo, Alvis Brazma, Inge Jonassen, Alan Robinson,
Esko Ukkonen,
Mining for Putative Regulatory Elements in the Yeast
Genome using Gene Expression Data
ISMB 2000, 384-394.
- Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM
Systematic determination of genetic network architecture.
Nat Genet 1999 Jul;22(3):281-5
- Hughes JD, Estep PW, Tavazoie S, Church GM.
Computational identification of cis-regulatory elements
associated with groups of functionally related genes in
Saccharomyces cerevisiae.
J Mol Biol. 2000 Mar 10;296(5):1205-14.
- J. Zhu and M. Q. Zhang,
Cluster, Function and Promoter: Analysis of Yeast
Expression Array
,
PSB 2000.
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| 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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