CSE Comp Bio group logo University of Washington Department of Computer Science & Engineering
 CSE 590 CB, Autumn 2003
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Reading and Research in Computational Biology
Mondays, 3:30 - 4:50, MEB 243

NOTE NEW ROOM ABOVE.

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:  Joe Felsenstein, Bill Noble, Larry Ruzzo, 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
09/29   Organizational meeting  
10/06 4 pm, PAA: Chao Tang Dynamic Properties of Biological Regulatory Networks Abstract
10/13 Koch, Wilamowska, Tompa Large scale comparative analyses Papers
10/20 Bar, Prakash, Noble Genome-scale design of PCR primers Paper
10/27 Yao, Noble Similarity among Tandem Mass Spectra Paper
11/03 Maynard Olson The Imprint of Balancing Selection on the Human Genome  
11/10 Bob Waterston Strategies for predicting functional genes  
11/17 Li, Wilamowska, Felsenstein Parametric phylogenetics and large phylogenies Papers
11/24 Klammer, Felsenstein The (super) tree of life: procedures, prospects, and problems Paper
12/01 Finney, Mercaldi, Ruzzo Predicting noncoding RNAs Paper
12/08 Weinberg, Ruzzo Predicting noncoding RNAs  

 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.  


10/6:

TITLE: Dynamic Properties of Biological Regulatory Networks

ABSTRACT: The interactions between proteins, DNA, and RNA in living cells constitute molecular networks that govern various cellular functions. To investigate the global dynamical properties and stabilities of such networks, we studied the cell-cycle regulatory network of the budding yeast. With the use of a simple dynamical model, it was demonstrated that the cell-cycle network is extremely stable and robust for its function. The biological stationary state-the G1 state-is a global attractor of the dynamics. The biological pathway-the cell-cycle sequence of protein states-is a globally attracting trajectory of the dynamics. These properties are largely preserved with respect to small perturbations to the network. These results suggest that cellular regulatory networks are robustly designed for their functions. This will be a pedagogical talk.

10/13:

Comparative analyses of multi-species sequences from targeted genomic regions , Thomas et al.

Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting , Paul Cliften, Priya Sudarsanam, Ashwin Desikan, Lucinda Fulton, Bob Fulton, John Majors, Robert Waterston, Barak A. Cohen, Mark Johnston

10/20:

Genome-scale design of PCR primers and long oligomers for DNA microarrays , Stefan A. Haas, Marc Hild, Anthony P. H. Wright, Torsten Hain, Driss Talibi and Martin Vingron

10/27:

Similarity among Tandem Mass Spectra from Proteomic Experiments: Detection, Significance, and Utility , David L. Tabb, Michael J. MacCoss, Christine C. Wu, Scott D. Anderson, and John R. Yates, III

11/17:

Parametric Phylogenetics? , M. J. Sanderson and J. Kim

Roshan, U., B. M. E. Moret, T. L. Williams, and T. Warnow. Iterative-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees. Manuscript, submitted for publication.
If you would like to read this paper in advance of the seminar, send a request to tompa@cs.washington.edu

11/24:

The (super) tree of life: procedures, prospects, and problems , O. R. P. Bininda-Emonds, J. L. Gittleman, and M. A. Steel

12/01:

Eddy & Durbin "RNA Sequence analysis using covariance models" Nucleic Acids Research v 22 #11, (1994) 2079-88. Preprint (NAR online doesn't go back that far)



 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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University of Washington
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