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  CSE 590CAu '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, EE1 026
Organizers: David Haynor, 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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 Theme This quarter's discussion will focus on, well, any interesting comp bio topics.
 Date  Presenters/Participants Topic Details
10/02---- Organizational Meeting ----
10/09Jacob, Ian, Ayse; LeeMedical-Expert-Level Deep LearningDetails
10/16Daniel; RuzzoRibosome FootprintingDetails
10/23Scott; NobleVisualizing ChromatinDetails
10/30Nao, Xingfan; KannanSingle-Cell EpigeneticsDetails
11/06Gabe; HaynorSingle-Cell Differentiation via RNASeqDetails
11/13Damon, Katie; RuzzoNanopore protein sequencingDetails
11/20Yue; WangStem Cell Differentiation as a Markov ProcessDetails
11/27Sudipto; KannanDevelopmental DifferentiationDetails
12/04Dave; Noble3D Super-Resolution Image ReconstructionDetails
 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.  

10/02:   -- ---- Organizational Meeting ----

10/09: Medical-Expert-Level Deep Learning -- Jacob, Ian, Ayse; Lee

  • A Esteva, B Kuprel, RA Novoa, J Ko, SM Swetter, HM Blau, S Thrun, "Corrigendum: Dermatologist-level classification of skin cancer with deep neural networks." Nature, 546, #7660 (2017) 686. [offcampus]
  • P Rajpurkar, AY Hannun, M Haghpanahi, C Bourn, AY Ng, "Cardiologist-Level Arrhythmia Detection with Convolutional Neural Networks."

10/16: Ribosome Footprinting -- Daniel; Ruzzo

10/23: Visualizing Chromatin -- Scott; Noble

  • HD Ou, S Phan, TJ Deerinck, A Thor, MH Ellisman, CC O'Shea, "ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells." Science, 357, #6349 (2017) . [offcampus]

10/30: Single-Cell Epigenetics -- Nao, Xingfan; Kannan

11/06: Single-Cell Differentiation via RNASeq -- Gabe; Haynor

11/13: Nanopore protein sequencing -- Damon, Katie; Ruzzo

11/20: Stem Cell Differentiation as a Markov Process -- Yue; Wang

  • PS Stumpf, RCG Smith, M Lenz, A Schuppert, FJ Müller, A Babtie, TE Chan, MPH Stumpf, CP Please, SD Howison, F Arai, BD MacArthur, "Stem Cell Differentiation as a Non-Markov Stochastic Process." Cell Syst, 5, #3 (2017) 268-282.e7. [offcampus]

11/27: Developmental Differentiation -- Sudipto; Kannan

12/04: 3D Super-Resolution Image Reconstruction -- Dave; Noble

 Other Papers Other suggested topics/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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University of Washington
Box 352350
Seattle, WA  98195-2350
(206) 543-1695 voice, (206) 543-2969 FAX