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  CSE 590CWi '17:  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, 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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 Theme This quarter's discussion will focus on both single-cell "omics" and nanopore sequencing.
 Date  Presenters/Participants Topic Details
01/09---- Organizational Meeting ----
01/23Sudipto, Shunfu; KannanSingle cell 1Details
01/30Jack; KannanSingle cell 2Details
02/06---- Canceled; Snow Day! ----
02/13Safiye, Katie, Nao; KannanSingle cell 3Details
02/27Eliah; RuzzoNanopore 1Details
03/06Jacob; RuzzoNanopore 2Details
 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.  

01/09:   -- ---- Organizational Meeting ----

01/16:   -- Holiday

01/23: Single cell 1 -- Sudipto, Shunfu; Kannan

    Learning dynamics and transcriptional network structure from single cell sequenced data.

01/30: Single cell 2 -- Jack; Kannan

  • M Setty, MD Tadmor, S Reich-Zeliger, O Angel, TM Salame, P Kathail, K Choi, S Bendall, N Friedman, D Pe'er, "Wishbone identifies bifurcating developmental trajectories from single-cell data." Nat. Biotechnol., 34, #6 (2016) 637-45. [offcampus]

02/06:   -- ---- Canceled; Snow Day! ----

02/13: Single cell 3 -- Safiye, Katie, Nao; Kannan

  • A Dixit, O Parnas, B Li, J Chen, CP Fulco, L Jerby-Arnon, ND Marjanovic, D Dionne, T Burks, R Raychowdhury, B Adamson, TM Norman, ES Lander, JS Weissman, N Friedman, et 1 al., "Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens." Cell, 167, #7 (2016) 1853-1866.e17. [offcampus]

02/20:   -- Holiday

02/27: Nanopore 1 -- Eliah; Ruzzo

03/06: Nanopore 2 -- Jacob; Ruzzo

 Other Papers Other suggested topics/papers that didn't fit the schedule:
  • Multi-omic data analysis; Molecular understanding of different cell types using omic data (roughly)
    • A review paper on multi-omics: Brief argument for/against this paper: Since it is a review paper, it covers the intuition behind the various methods more than the detail of each. This could be a nice way to open the quarter, but it definitely lacks some computational depth.
    • A paper covering a multi-outcome GWAS on insulin resistance.
      • LA Lotta, P Gulati, FR Day, F Payne, H Ongen, M van de Bunt, KJ Gaulton, JD Eicher, SJ Sharp, J Luan, E De Lucia Rolfe, ID Stewart, E Wheeler, SM Willems, C Adams, et 17 al., "Integrative genomic analysis implicates limited peripheral adipose storage capacity in the pathogenesis of human insulin resistance." Nat. Genet., 49, #1 (2017) 17-26. [offcampus]
      Pros: Rather than check association with a single outcome, this paper does GWAS against multiple phenotypes as a surrogate for a more invasive phenotype. They seem to followup the association study with interesting results that demonstrate how to followup on SNPs to get mechanistic insight. Cons: I have not delved into the math yet so I don't know how interesting it will be.
    • An interesting paper presenting an integrative analysis showing that disease-associated GWAS variants perturb tissue-specific regulatory modules:
  • Deep learning applications in computational biology:
 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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