CSE Comp Bio group logo University of Washington Department of Computer Science & Engineering
 CSE 590 CB, Winter 2002
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Reading and Research in Computational Biology
Mondays, 3:30 - 4:50, EE 003

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.
Organizers:  Larry Ruzzo, Rimli Sengupta, 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
01/07 Organizational Meeting    
01/14 Tony Hazbun, Genome Sciences Genome-wide identification of yeast transcription factors  
01/21 Holiday    
01/28 Jared Roach, ISB fugu Annotation Challenges  
02/04 Brian Tjaden, CSE Identifying operons and untranscribed regions of transcripts using Escherichia coli RNA expression analysis Abstract
02/11 Jim Holloway, ZymoGenetics Computational biology at ZymoGenetics with Family ORiented GEnomic Threading (FORGET) as an example Abstract
02/18 Holiday    
02/25 Bill Noble, Columbia & UW Bioinformatics Classification: Protein Function, Gene Expression and Cancer Subtypes  
03/04 Jaeger, Grossman, Tjaden & Yao "Probabilistic Hierarchical Clustering for Biological Data," E. Segal & D. Koller. To appear RECOMB '02  
03/11 Blanchette, Kang, Prakash, Rocke, Shavit, Shefner, & Weinberg "Finding Motifs in the Twilight Zone," U. Keich & P. Pevzner. To appear RECOMB '02  

 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.  


2/4:   Identifying operons and untranscribed regions of transcripts using Escherichia coli RNA expression analysis

Brian Tjaden, UW CSE

Abstract: Microarrays traditionally have been used to assay the transcript expression of coding regions of genes. Here, we use Escherichia coli oligonucleotide microarrays to assay transcript expression of both open reading frames (ORFs) and intergenic regions. We then use hidden Markov models to analyze this expression data and estimate transcription boundaries of genes. This approach allows us to identify 5' untranslated regions (UTRs) of transcripts as well as genes which are likely to be operon members. The operon elements we identify correspond to documented operons with 99% specificity and 63% sensitivity. Similarly we find that our 5' UTR results accurately coincide with experimentally verified promoter regions for most genes.

Joint work with: David Haynor (UW); Sergey Stolyar and Eugene Kolker (ISB); Carsten Rosenow and Rini Mukherjee Saxena (Affymetrix).


2/11:   Computational biology at ZymoGenetics with Family ORiented GEnomic Threading (FORGET) as an example

Jim Holloway, ZymoGenetics

Abstract: I will briefly discuss my work environment at ZymoGenetics followed by a discussion of a process developed recently to find novel, potentially therapeutic, proteins in genomic sequence that other gene prediction programs may have missed.



 Other  Seminars Applied Math Department Mathematical Biology Journal Club
Biostatistics Seminars
Biochemistry Department Seminars
COMBI & Other Genome Sciences Seminars
Microbiology Department Seminars
Zoology 525, Mathematical Biology Seminar Series

 Resources MBT/GENET 540/541: Introduction to Computational Molecular Biology: Genome and Protein Sequence Analysis
CSE 527 (Computational Biology) (formerly known as CSE 590 BI).


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