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Course Info |
CSE 590C is a weekly seminar on Readings and Research in
Computational Biology, open to all graduate students in computational,
biological, and mathematical sciences.
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Schedule |
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Papers, etc. |
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,
follow the "[offcampus]" links below or
look at the
library "proxy server" instructions.
You will be prompted for your UW net ID and password once per
session.
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Abstract: A basic operation in biological sequence analysis is the comparison of sequences derived from the environment ("query sequences") to previously-characterized sequences ("reference sequences"). Some analyses are especially time-intensive when the number of reference sequences is large, motivating a way to reduce the number of reference sequences while maintaining a subset that maintains the relevant span of diversity of the reference sequences. We have formalized an objective function for this reduction in terms of the minimization of the average distance to the closest leaf in a phylogenetic tree. To optimize this objective function, we show that the greedy algorithm is not effective, show that a variant of the classical Partitioning Among Medoids (PAM) heuristic gets stuck in local minima, and develop an exact dynamic programming approach. Our formulation of the exact algorithm, which uses ideas from convex geometry, is time-competitive with the heuristic approach. This talk will introduce these ideas, guided by our motivating example, which is the detection of "superinfection" (secondary infection) in HIV. |
10/08: Regulation in Plasmodium -- Emilia, Qian; Noble
10/15: Molecular modeling of protein-nucleic acid interactions -- Phil Bradley, FHCRC
10/22: Noncoding RNA in ENCODE -- John, Peter; Ruzzo
10/29: The Perils of Correlation Analysis -- Miles, Phil; Borenstein
11/05: Personalized Omics -- Sonya, Daniel; Lee (& Haynor)
11/12: -- Holiday
11/19: Pattern Discovery via Multitrack Segmentation -- Maxim, Alex; Bolouri
11/26: Genomic Cancer Drivers -- Jeremy, Patricio; Lee
12/03: Transcription Factor Variation -- Paul, Max; Tompa
CSE's Computational Molecular Biology research group
Interdisciplinary Ph.D. program in Computational Molecular Biology
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Computer Science & Engineering University of Washington Box 352350 Seattle, WA 98195-2350 (206) 543-1695 voice, (206) 543-2969 FAX |