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 CSE 590 CB, Wi '05: Reading & Research in Comp. Bio.
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 Course Info    CSE 590CB is a weekly seminar on Readings and Research in Computational Biology, open to all graduate students in computational, biological, and mathematical sciences.
When/Where:  Mondays, 3:30 - 4:50, EE1 025
Organizers:  Joe Felsenstein, Michal Linial, Bill Noble, Emily Rocke, Larry Ruzzo, Martin Tompa
Credit: 1-3 Variable
Grading: Credit/No Credit. Talk to the organizers if you are unsure of our expectations.
 Email
cse590cb@cs.washington.edu Course-related announcements and discussions
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compbio-group@cs.washington.edu Discussions about computational biology
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 Schedule
 Date  Presenters/Participants Topic Papers
01/03   ---- Organizational Meeting ----  
01/10 Brig, Nan (Michal) Alternative Splicing Papers
01/17   --- Holiday ---  
01/24 Zizhen (Larry) RNA Folding Paper
01/31 Ross, Jonathon (Bill) Shotgun Mass Spec Paper
02/07 Mathias, Mukund (Emily) Multiple Sequence Alignment: Basics Papers
02/14 Zasha (Joe) Multiple Sequence Alignment: With phylogeny Papers
02/21   --- Holiday ---  
02/28 Becky (Emily) Multiple Sequence Alignment: Genome-scale Papers
03/07 Amol, Mike (Martin) Conserved Non-coding Sequences Papers

 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.

During Autumn 2004, the Library deployed a new proxy server; if you are accessing this page from an offcampus computer, the "[offcampus]" links below may be more convenient. You will be prompted for your UW net ID and password once per session.  


01/10: Alternative Splicing -- Brig, Nan (Michal)

    Abstract:  A combination of experimental and bioinformatics approaches leads Burge and colleagues (Wang et al., 2004 [this issue of Cell]) to a global view of how an RNA segment may be selected or avoided in mature mRNAs due to biased distributions of exonic enhancers and silencers, a process vital for genome evolution, developmental control, and disease onset.
  • Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, Burge CB, Systematic identification and analysis of exonic splicing silencers, Cell. 2004 Dec 17;119(6):831-45

    Abstract:  Exonic splicing silencers (ESSs) are cis-regulatory elements that inhibit the use of adjacent splice sites, often contributing to alternative splicing (AS). To systematically identify ESSs, an in vivo splicing reporter system was developed to screen a library of random decanucleotides. The screen yielded 141 ESS decamers, 133 of which were unique. The silencer activity of over a dozen of these sequences was also confirmed in a heterologous exon/intron context and in a second cell type. Of the unique ESS decamers, most could be clustered into groups to yield seven putative ESS motifs, some resembling known motifs bound by hnRNPs H and A1. Potential roles of ESSs in constitutive splicing were explored using an algorithm, ExonScan, which simulates splicing based on known or putative splicing-related motifs. ExonScan and related bioinformatic analyses suggest that these ESS motifs play important roles in suppression of pseudoexons, in splice site definition, and in AS.

01/17: --- Holiday --- --  

01/24: RNA Folding -- Zizhen (Larry)

01/31: Shotgun Mass Spec -- Ross, Jonathon (Bill)

02/07: Multiple Sequence Alignment: Basics -- Mathias, Mukund (Emily)

  • Thompson J.D., Higgins D.G., Gibson T.J.(1994), CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting,position-specific gap penalties and weight matrix choice, Nucleic Acids Res. 22:4673-4680 [offcampus]

02/14: Multiple Sequence Alignment: With phylogeny -- Zasha (Joe)

02/21: --- Holiday --- --  

02/28: Multiple Sequence Alignment: Genome-scale -- Becky (Emily)

  • Mathieu Blanchette, W. James Kent, Cathy Riemer, Laura Elnitski, Arian F.A. Smit, Krishna M. Roskin, Robert Baertsch, Kate Rosenbloom, Hiram Clawson, Eric D. Green, David Haussler, and Webb Miller, Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner, Genome Res., Apr 2004; 14: 708 - 715 [offcampus]

03/07: Conserved Non-coding Sequences -- Amol, Mike (Martin)

  • Elliott H. Margulies, Mathieu Blanchette, NISC Comparative Sequencing Program, David Haussler and Eric D. Green, Identification and Characterization of Multi-Species Conserved Sequences, Genome Research 13:2507-2518, 2003 [offcampus]

 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
A very comprehensive FAQ at bioinformatics.org, including annotated references to online tutorials and lectures.
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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Box 352350
Seattle, WA  98195-2350
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