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Reading and Research in Computational Biology
CSE 590CB is a weekly seminar on Readings and Research in
Computational Biology, open to all graduate students in the computer,
biological, and mathematical sciences.
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| Organizers: | Bill Noble, Martin Tompa |
| Credit: | 1-3 Variable |
| Grading: | Credit/No Credit. Talk to the organizers if you are unsure of our expectations. |
Related Email Lists:
compbio-seminars@cs.washington.edu:
biology seminar announcements from all around campus.
compbio-group@cs.washington.edu:
discussions about computational biology.
To subscribe, send a message to
majordomo@cs.washington.edu
whose body (not subject) is the line
subscribe groupname
where groupname is either
compbio-group or compbio-seminars
| Date | Presenters/Participants | Topic | Papers |
|---|---|---|---|
| 03/31 | Organizational meeting | ||
| 04/07 | Brian Tjaden | Identifying transcripts in intergenic regions using E. coli oligonucleotide arrays | Abstract |
| 04/14 | David Baker, UW Biochemistry | Protein structure prediction and design | |
| 04/21 | Joe Felsenstein, UW Genome Sciences | Thinking about inferring phylogenies from multiple genes | Abstract |
| 04/28 | Zasha Weinberg | "Do principal axes of inertia predict proteins active sites?" and "Are insect proteins exported to their obligate endosymbionts?" | Abstract |
| 05/05 | Vassili Sukharev | ||
| 05/12 | Tom Daniel, UW Biology | Modelling many molecular motors, mostly in muscle | Paper |
| 05/19 | Emily Rocke | Explorations of the olfactory gene family in C. elegans | Abstract |
| 05/26 | Memorial Day Holiday | ||
| 06/02 | Richard Ladner | Context-Free Grammars for Compressing and Finding Structure in DNA | |
Note on Electronic Access to Journals
TITLE: Identifying Transcripts in Intergenic Regions Using E. coli Oligonucleotide Arrays
ABSTRACT:
Microarrays traditionally have been used to assay the transcript
expression of coding regions of genes. Using Escherichia coli
oligonucleotide arrays, we present a high-throughput method for transcript
discovery focused mainly on intergenic regions. This approach allows us to
identify over 1000 intergenic transcripts in E. coli, including
untranslated regions (UTRs) of genes, operons, and small RNAs. We will
present some interesting biological applications of this work as well as
some of the computational challenges faced in using microarrays to
identify non-coding transcripts.
4/21:
TITLE: Thinking about inferring phylogenies from multiple genes
ABSTRACT:
As the volume of data has increased in molecular biology, molecular
evolutionists have increasingly faced the issue of how to combine data
from multiple gene loci. A controversy has arisen as to whether the
data should be combined into one analysis, or whether the resulting trees
should instead be combined by consensus tree methods. I will look at the
problem and present a method that has elements of a compromise, which
arises naturally when we model the variation of processes from locus to
locus. The matter is complicated by the fact that we may not actually
have the same tree in all loci, owing to coalescence phenomena.
4/28:
TITLE: "Do principal axes of inertia predict proteins' active sites?" and "Are insect proteins exported to their obligate endosymbionts?"
ABSTRACT:
I will be talking about 2 small projects I've worked on in
the last year. The first has to do with determining if the principal
axes of inertia (a concept in Newtonian mechanics) is a significant
factor when proteins bind to small molecules. The second talk deals
with species of symbiotic bacteria that live inside specialized-cells
of insects. I discuss a simple computational strategy for
understanding how the insect might provide for the needs of these
bacteria by expressing genes whose proteins are used by the bacteria.
Both projects are still in progress.
5/12:
TITLE: Modelling many molecular motors, mostly in muscle
TITLE: Explorations of the olfactory gene family in C. elegans
ABSTRACT: In the worm C. elegans and its close relative C. briggsae, the olfactory gene family is a family of several hundred genes that allow the worm to sense various chemicals. In this talk I will discuss computational issues related to discovering and analyzing members of the gene family and their promoters.
CSE's Computational Molecular Biology research group
Interdisciplinary Ph.D. program in Computational Molecular Biology
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Department of Computer Science & Engineering University of Washington Box 352350 Seattle, WA 98195-2350 (206) 543-1695 voice, (206) 543-2969 FAX [comments to cse590cb-webmaster@cs.washington.edu] | |