CSE 590C,  Au '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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Schedule		Date  Presenters/Participants Topic Details 09/24 ---- Organizational Meeting ---- 10/01 Erick Matsen, FHCRC HIV superinfection and an exact solution to the k-medoids problem on phylogenetic trees Details 10/08 Emilia, Qian; Noble Regulation in Plasmodium Details 10/15 Phil Bradley, FHCRC Molecular modeling of protein-nucleic acid interactions Details 10/22 John, Peter; Ruzzo Noncoding RNA in ENCODE Details 10/29 Miles, Phil; Borenstein The Perils of Correlation Analysis Details 11/05 Sonya, Daniel; Lee (& Haynor) Personalized Omics Details 11/12 Holiday 11/19 Maxim, Alex; Bolouri Pattern Discovery via Multitrack Segmentation Details 11/26 Jeremy, Patricio; Lee Genomic Cancer Drivers Details 12/03 Paul, Max; Tompa Transcription Factor Variation Details
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. Slides: http://matsen.github.com/talks/121001_cse_530c.html [offcampus] Paper: http://arxiv.org/pdf/1205.6867v2.pdf [offcampus] 10/08: Regulation in Plasmodium -- Emilia, Qian; Noble R Jurgelenaite, TM Dijkstra, CH Kocken, T Heskes, "Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum." Bioinformatics, 25, #12 (2009) 1484-91. [offcampus] and/or J Wu, DH Sieglaff, J Gervin, XS Xie, "Discovering regulatory motifs in the Plasmodium genome using comparative genomics." Bioinformatics, 24, #17 (2008) 1843-9. [offcampus] 10/15: Molecular modeling of protein-nucleic acid interactions -- Phil Bradley, FHCRC AN Mak, P Bradley, RA Cernadas, AJ Bogdanove, BL Stoddard, "The crystal structure of TAL effector PthXo1 bound to its DNA target." Science, 335, #6069 (2012) 716-9. [offcampus] LA Liu, P Bradley, "Atomistic modeling of protein-DNA interaction specificity: progress and applications." Curr. Opin. Struct. Biol., 22, #4 (2012) 397-405. [offcampus] 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 MM Hoffman, OJ Buske, J Wang, Z Weng, JA Bilmes, WS Noble, "Unsupervised pattern discovery in human chromatin structure through genomic segmentation." Nat. Methods, 9, #5 (2012) 473-6. [offcampus] 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 bioinformatics.org, 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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