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  CSE 590CAu '21:  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, LOW 111 (and by zoom)
Zoom Link:
Organizers: Su-In Lee, Wouter Meuleman, Sara Mostafavi, Larry Ruzzo, Sheng 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 (loosely) on, well, any interesting comp bio topics.
 Date  Presenters/Participants Topic Details
10/04---- Organizational Meeting ---- Video
10/11No Class
10/18Ayse, Chris; RuzzoBenchmark BiasesDetails;  Video
10/25Addie, ErinOptimizing Protein ProductionDetails;  Slides;  Video;  Chat
11/01Anna, PascalPerils of Dimension ReductionDetails;  Slides;  Video;  Chat
11/08Gian Marco; RuzzoHierarchical HypothesesDetails;  Slides;  Video
11/15EthanContrastive PCADetails;  Slides;  Video
11/22Alyssa; MeulemanSequence -> Function: RegulationDetails;  Video;  Chat
11/29Ian, Xinming; MostafaviSequence -> Function: Enhancer-Promoter Interactions & ATAC-seqDetails;  Slides;  Video;  Chat
12/06Bingbing; MostafaviSequence -> Function: Chromatin Accessibility & Histone ModsDetails;  Slides;  Video
 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.  

10/04:   -- ---- Organizational Meeting ----

10/11:   -- No Class

10/18: Benchmark Biases -- Ayse, Chris; Ruzzo

10/25: Optimizing Protein Production -- Addie, Erin

  • Caitlin Gamble, Drew Bryant, Damian Carrieri, Eli Bixby, Jason Dang, Jacob Marshall, David Doughty, Lucy Colwell, Marc Berndl, James Roberts, Michael Frumkin, "Machine Learning Optimization of Photosynthetic Microbe Cultivation and Recombinant Protein Production,"

11/01: Perils of Dimension Reduction -- Anna, Pascal

11/08: Hierarchical Hypotheses -- Gian Marco; Ruzzo

11/15: Contrastive PCA -- Ethan

11/22: Sequence -> Function: Regulation -- Alyssa; Meuleman

11/29: Sequence -> Function: Enhancer-Promoter Interactions & ATAC-seq -- Ian, Xinming; Mostafavi

12/06: Sequence -> Function: Chromatin Accessibility & Histone Mods -- Bingbing; Mostafavi

 Other Papers Other suggested topics/papers:
 Other Seminars Past quarters of CSE 590C
COMBI & Genome Sciences Seminars
 Resources Molecular Biology for Computer Scientists, a primer by Lawrence Hunter (46 pages)
A comprehensive FAQ at, including annotated links to online tutorials and lectures.
CSE 527: Computational Biology
CSEP 527: 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