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  CSE 590CWi '22:  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, (By Zoom, until further notice.)
Zoom Link:
Organizers: Su-In Lee, Wouter Meuleman, Sara Mostafavi, Bill Noble, Larry Ruzzo, Sheng Wang, and ???
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... a theme to be determined by you, the participants.
We welcome participation by everyone in the CMB community, broadly construed, and especially students. Unclaimed papers suggested so far (no particular order):
 Videos Video recordings of all Zoom presentations are here.
 Date  Presenters/Participants Topic Details
01/03---- Organizational Meeting ---- Chat
01/10Lee; RuzzoLewontin's ParadoxDetails;  Slides
01/24No Class: Instead, check out Wednesday's Combi Seminar.
01/31No Class
02/07Ayse, Nicasia; MostafaviSingle Cell ClusteringDetails;  Slides
02/14Bing Bing; RuzzoDeep Learning and RNA structureDetails;  Slides
02/28Pascal; WangUnsupervised Transformers Learn Protein StructuresDetails
03/07AlyssaProtein FitnessDetails;  Slides
 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.  

01/03:   -- ---- Organizational Meeting ----

01/10: Lewontin's Paradox -- Lee; Ruzzo

01/17:   -- Holiday

01/24:   -- No Class: Instead, check out Wednesday's Combi Seminar.

01/31:   -- No Class

02/07: Single Cell Clustering -- Ayse, Nicasia; Mostafavi

02/14: Deep Learning and RNA structure -- Bing Bing; Ruzzo

02/21:   -- Holiday

02/28: Unsupervised Transformers Learn Protein Structures -- Pascal; Wang

03/07: Protein Fitness -- Alyssa

 Other Papers Other suggested topics/papers:
  • Sara suggested finding some paper(s) on single-cell omics; Larry happened to bump into this review-ish article recently, but there may be better papers for the purpose
  • Wouter suggested the following review paper
  • Larry added
    • T Stoeger, LA Nunes Amaral, "The characteristics of early-stage research into human genes are substantially different from subsequent research." PLoS Biol, 20, #1 (2022) e3001520.
 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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