CSE Comp Bio group logo University of Washington Department of Computer Science & Engineering
 CSE 590 CB, Spring 2003
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Reading and Research in Computational Biology
Mondays, 3:30 - 4:50, EE1 026

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.
Organizers:  Bill Noble, Martin Tompa
Credit: 1-3 Variable
Grading: Credit/No Credit. Talk to the organizers if you are unsure of our expectations.
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 Schedule
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  

 Papers, etc.

  Note on Electronic Access to Journals

Links to full papers below are often to journals that require a paid subscription. The UW Library is generally a paid subscriber, and you can freely access these articles if you do so from an on-campus computer. For off-campus access, look at the library "proxy server" instructions.  


4/7:

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

Here is the paper.

5/19:

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.



 Other  Seminars Past quarters of CSE 590CB
COMBI & Genome Sciences Seminars
Applied Math Department Mathematical Biology Journal Club
Biostatistics Seminars
Microbiology Department Seminars
Zoology 525, Mathematical Biology Seminar Series

 Resources Molecular Biology for Computer Scientists, a primer by Lawrence Hunter (46 pages)
A Quick Introduction to Elements of Biology, a primer by Alvis Brazma et al.
S-Star Bioinformatics Online Course Schedule, a collection of video primers
CSE 527: Computational Biology
CSE 590TV: Computational Biology (Professional Masters Program)
Genome 540/541: Introduction to Computational Molecular Biology: Genome and Protein Sequence Analysis

CSE's Computational Molecular Biology research group
Interdisciplinary Ph.D. program in Computational Molecular Biology


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University of Washington
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Seattle, WA  98195-2350
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