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  CSE 590CAu '16:  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 054
Organizers: Joe Felsenstein, Sreeram Kannan, Su-In Lee, Bill Noble, Larry Ruzzo, Yuliang Wang
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
10/03---- Organizational Meeting ----
10/10Katie; RuzzoRNAseq BenchmarksDetails
10/17Scott; RuzzoVariant Calling BenchmarksDetails
10/24Alex; LeeSingle-cell RNA-seq in melanomaDetails
10/31Cody, Pat; NoblePredicting Ribosome FootprintsDetails
11/07Arman, Jacob; NobleFunctional relationships from DNA contact mapsDetails
11/14Daniel; HaynorSynthetic lethality and other genetic interactionsDetails
11/21Dave, Farah; NobleDeep learning for circadian rythmsDetails
11/28Safiye; WangHistone Methylation and MetabolismDetails
12/05Damon; KannanMulti-trait predictionDetails
 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.  

10/03:   -- ---- Organizational Meeting ----

10/10: RNAseq Benchmarks -- Katie; Ruzzo

  • M Teng, MI Love, CA Davis, S Djebali, A Dobin, BR Graveley, S Li, CE Mason, S Olson, D Pervouchine, CA Sloan, X Wei, L Zhan, RA Irizarry, "A benchmark for RNA-seq quantification pipelines." Genome Biol., 17, (2016) 74. [offcampus]
  • M Teng, MI Love, CA Davis, S Djebali, A Dobin, BR Graveley, S Li, CE Mason, S Olson, D Pervouchine, CA Sloan, X Wei, L Zhan, RA Irizarry, "Erratum to: A benchmark for RNA-seq quantification pipelines." Genome Biol., 17, #1 (2016) 107. [offcampus]

10/17: Variant Calling Benchmarks -- Scott; Ruzzo

  • S Hwang, E Kim, I Lee, EM Marcotte, "Systematic comparison of variant calling pipelines using gold standard personal exome variants." Sci Rep, 5, (2015) 17875. [offcampus]

10/24: Single-cell RNA-seq in melanoma -- Alex; Lee

  • I Tirosh, B Izar, SM Prakadan, MH Wadsworth, D Treacy, JJ Trombetta, A Rotem, C Rodman, C Lian, G Murphy, M Fallahi-Sichani, K Dutton-Regester, JR Lin, O Cohen, P Shah, et 22 al., "Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq." Science, 352, #6282 (2016) 189-96. [offcampus]

10/31: Predicting Ribosome Footprints -- Cody, Pat; Noble

11/07: Functional relationships from DNA contact maps -- Arman, Jacob; Noble

11/14: Synthetic lethality and other genetic interactions -- Daniel; Haynor

11/21: Deep learning for circadian rythms -- Dave, Farah; Noble


11/28: Histone Methylation and Metabolism -- Safiye; Wang

This (not yet peer reviewed) paper describes a new computational analysis integrating DNA methylation and gene expression data from The Cancer Genome Atlas to predict both overall and locus-specific DNA methylation levels based on the expression of key metabolic genes:

A somewhat related paper (more experimental than computational) could be an interesting read - it relates metabolic perturbation and histone methylation:
  • SJ Mentch, M Mehrmohamadi, L Huang, X Liu, D Gupta, D Mattocks, P G√≥mez Padilla, G Ables, MM Bamman, AE Thalacker-Mercer, SN Nichenametla, JW Locasale, "Histone Methylation Dynamics and Gene Regulation Occur through the Sensing of One-Carbon Metabolism." Cell Metab., 22, #5 (2015) 861-73. [offcampus]

12/05: Multi-trait prediction -- Damon; Kannan

 Other Papers Other suggested papers that didn't fit the schedule:
 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, 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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