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Reading and Research in Computational Biology
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.
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| 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. |
| 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 | |
Note on Electronic Access to Journals
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).
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.
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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] | |