CSE 590C,  Au '15:  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, EE1 031 Organizers:  Joe Felsenstein, Sreeram Kannan, Su-In Lee, Bill Noble, Larry Ruzzo, Cole Trapnell Credit:  1-3 Variable Grading:  Credit/No Credit. Talk to the organizers if you are unsure of our expectations.
Email		cse590cb@cs.washington.edu Course-related announcements and discussions   Manage Your Subscription List Archives compbio-seminars@cs.washington.edu Biology seminar announcements from all around campus   Manage Your Subscription List Archives compbio-group@cs.washington.edu Computational biology discussions, conference/job postings, etc.,   Manage Your Subscription List Archives
Schedule		Date  Presenters/Participants Topic Details 10/05 ---- Organizational Meeting ---- 10/12 Nikolai; Felsenstein Protein Evolution & Dynamics Details 10/19 Jack & Jacob; Noble Chromatin Structure Details 10/26 Max & Alex; Noble Metabolome MS/MS Details 11/02 Scott; Haynor PrediXcan Details 11/09 Katie & Nao; Ruzzo Noncoding RNA Evolution Details 11/16 Safiye; Lee Predicting Drug Response Details 11/23 Daniel; Ruzzo Human/Mouse Co-Expression(?) Details 11/30 Sven & Rahul; Lee Regulation in Cancer Details 12/07 Shunfu; Kannan Single-Cell Expression Details
Papers, etc.		Note on Electronic Access to Journals The UW Library is generally a paid subscriber to non-open-access journals we cite. You can freely access these articles from on-campus computers. 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.   10/05:   -- ---- Organizational Meeting ---- 10/12: Protein Evolution & Dynamics -- Nikolai; Felsenstein H Edwards, CM Deane, "Structural Bridges through Fold Space." PLoS Comput. Biol., 11, #9 (2015) e1004466. T Sikosek, E Bornberg-Bauer, HS Chan, "Evolutionary dynamics on protein bi-stability landscapes can potentially resolve adaptive conflicts." PLoS Comput. Biol., 8, #9 (2012) e1002659. 10/19: Chromatin Structure -- Jack & Jacob; Noble R Mourad, O Cuvier, "Predicting the spatial organization of chromosomes using epigenetic data." Genome Biol., 16, (2015) 182. [offcampus] 10/26: Metabolome MS/MS -- Max & Alex; Noble H Tsugawa, T Cajka, T Kind, Y Ma, B Higgins, K Ikeda, M Kanazawa, J VanderGheynst, O Fiehn, M Arita, "MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis." Nat. Methods, 12, #6 (2015) 523-6. [offcampus] 11/02: PrediXcan -- Scott; Haynor ER Gamazon, HE Wheeler, KP Shah, SV Mozaffari, K Aquino-Michaels, RJ Carroll, AE Eyler, JC Denny, GTEx Consortium, DL Nicolae, NJ Cox, HK Im, "A gene-based association method for mapping traits using reference transcriptome data." Nat. Genet., 47, #9 (2015) 1091-8. [offcampus] 11/09: Noncoding RNA Evolution -- Katie & Nao; Ruzzo A Necsulea, M Soumillon, M Warnefors, A Liechti, T Daish, U Zeller, JC Baker, F Grützner, H Kaessmann, "The evolution of lncRNA repertoires and expression patterns in tetrapods." Nature, 505, #7485 (2014) 635-40. [offcampus] H Hezroni, D Koppstein, MG Schwartz, A Avrutin, DP Bartel, I Ulitsky, "Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species." Cell Rep, 11, #7 (2015) 1110-22. [offcampus] 11/16: Predicting Drug Response -- Safiye; Lee N Zhang, H Wang, Y Fang, J Wang, X Zheng, XS Liu, "Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model." PLoS Comput. Biol., 11, #9 (2015) e1004498. 11/23: Human/Mouse Co-Expression(?) -- Daniel; Ruzzo S Lin, Y Lin, JR Nery, MA Urich, A Breschi, CA Davis, A Dobin, C Zaleski, MA Beer, WC Chapman, TR Gingeras, JR Ecker, MP Snyder, "Comparison of the transcriptional landscapes between human and mouse tissues." Proc. Natl. Acad. Sci. U.S.A., 111, #48 (2014) 17224-9. [offcampus] Y Gilad, O Mizrahi-Man, "A reanalysis of mouse ENCODE comparative gene expression data." F1000Res, 4, (2015) 121. [offcampus] 11/30: Regulation in Cancer -- Sven & Rahul; Lee P Jiang, ML Freedman, JS Liu, XS Liu, "Inference of transcriptional regulation in cancers." Proc. Natl. Acad. Sci. U.S.A., 112, #25 (2015) 7731-6. [offcampus] 12/07: Single-Cell Expression -- Shunfu; Kannan PV Kharchenko, L Silberstein, DT Scadden, "Bayesian approach to single-cell differential expression analysis." Nat. Methods, 11, #7 (2014) 740-2. [offcampus]
Other Seminars		Past quarters of CSE 590C COMBI & Genome Sciences Seminars 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 comprehensive FAQ at bioinformatics.org, including annotated links to online tutorials and lectures. CSE 527: Computational Biology 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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