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| Course Info |
Reading and Research in Computational Biology
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| 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. |
Related Email Lists:
| compbio-seminars@cs.washington.edu | Biology seminar announcements from all around campus | Subscribe or unsubscribe |
| compbio-group@cs.washington.edu | Discussions about computational biology | Subscribe or unsubscribe |
| 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 | |
Note on Electronic Access to Journals
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)
CSE's Computational Molecular Biology research group
Interdisciplinary Ph.D. program in Computational Molecular Biology
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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] | |