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  CSE 590CAu '12:  Reading & Research in Comp. Bio.
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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.
When/Where:  Mondays, 3:30 - 4:50, EEB 042 (schematic)
Organizers:  Hamid Bolouri, Elhanan Borenstein, Su-In Lee, 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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 Date  Presenters/Participants Topic Details
09/24---- Organizational Meeting ----
10/01Erick Matsen, FHCRCHIV superinfection and an exact solution to the k-medoids problem on phylogenetic treesDetails
10/08Emilia, Qian; NobleRegulation in PlasmodiumDetails
10/15Phil Bradley, FHCRCMolecular modeling of protein-nucleic acid interactionsDetails
10/22John, Peter; RuzzoNoncoding RNA in ENCODEDetails
10/29Miles, Phil; BorensteinThe Perils of Correlation AnalysisDetails
11/05Sonya, Daniel; Lee (& Haynor)Personalized OmicsDetails
11/19Maxim, Alex; BolouriPattern Discovery via Multitrack SegmentationDetails
11/26Jeremy, Patricio; LeeGenomic Cancer DriversDetails
12/03Paul, Max; TompaTranscription Factor VariationDetails

 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, 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.  

09/24: ---- Organizational Meeting ----

10/01: HIV superinfection and an exact solution to the k-medoids problem on phylogenetic trees -- Erick Matsen, FHCRC

   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

  • T Derrien, R Johnson, G Bussotti, A Tanzer, S Djebali, H Tilgner, G Guernec, D Martin, A Merkel, DG Knowles, J Lagarde, L Veeravalli, X Ruan, Y Ruan, T Lassmann, et 12 al., "The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression." Genome Res., 22, #9 (2012) 1775-89. [offcampus]

10/29: The Perils of Correlation Analysis -- Miles, Phil; Borenstein

  • Friedman and Alm, "Inferring Correlation Networks from Genomic Survey Data", PLoS Comp Biol V8, No 9, e1002687

11/05: Personalized Omics -- Sonya, Daniel; Lee (& Haynor)

  • R Chen, GI Mias, J Li-Pook-Than, L Jiang, HY Lam, R Chen, E Miriami, KJ Karczewski, M Hariharan, FE Dewey, Y Cheng, MJ Clark, H Im, L Habegger, S Balasubramanian, et 26 al., "Personal omics profiling reveals dynamic molecular and medical phenotypes." Cell, 148, #6 (2012) 1293-307. [offcampus]

11/12:   -- Holiday

11/19: Pattern Discovery via Multitrack Segmentation -- Maxim, Alex; Bolouri

11/26: Genomic Cancer Drivers -- Jeremy, Patricio; Lee

  • UD Akavia, O Litvin, J Kim, F Sanchez-Garcia, D Kotliar, HC Causton, P Pochanard, E Mozes, LA Garraway, D Pe'er, "An integrated approach to uncover drivers of cancer." Cell, 143, #6 (2010) 1005-17. [offcampus]

12/03: Transcription Factor Variation -- Paul, Max; Tompa

  • M Spivakov, J Akhtar, P Kheradpour, K Beal, C Girardot, G Koscielny, J Herrero, M Kellis, EE Furlong, E Birney, "Analysis of variation at transcription factor binding sites in Drosophila and humans." Genome Biol., 13, #9 (2012) R49. [offcampus]

 Other  Seminars Past quarters of CSE 590C
COMBI & Genome Sciences Seminars
Applied Math Department Mathematical Biology Journal Club
Biostatistics Seminars
Microbiology Department Seminars

 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.
A very comprehensive FAQ at, including annotated references to online tutorials and lectures.
CSE 527: Computational Biology
CSE 590TV/CSEP 590A: 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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