CSE 590C,  Wi '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:  https://washington.zoom.us/j/99098776715 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.
Email		cse590cb@cs.washington.edu Course-related announcements and discussions   Manage Your Subscription List Archives compbio-seminars@cs.washington.edu Biology seminar announcements from all around campus   Manage Your Subscription List Archives compbio-group@cs.washington.edu Computational biology discussions, conference/job postings, etc.,   Manage Your Subscription List Archives
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.
Schedule		Date  Presenters/Participants Topic Details 01/03 ---- Organizational Meeting ----  Chat 01/10 Lee; Ruzzo Lewontin's Paradox Details;  Slides 01/17 Holiday 01/24 No Class: Instead, check out Wednesday's Combi Seminar. 01/31 No Class 02/07 Ayse, Nicasia; Mostafavi Single Cell Clustering Details;  Slides 02/14 Bing Bing; Ruzzo Deep Learning and RNA structure Details;  Slides 02/21 Holiday 02/28 Pascal; Wang Unsupervised Transformers Learn Protein Structures Details 03/07 Alyssa Protein Fitness Details;  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 DA Filatov, "Extreme Lewontin's Paradox in Ubiquitous Marine Phytoplankton Species." Mol Biol Evol, 36, #1 (2019) 4-14. [offcampus] 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 Z Hu, AA Ahmed, C Yau, "CIDER: an interpretable meta-clustering framework for single-cell RNA-seq data integration and evaluation." Genome Biol, 22, #1 (2021) 337. [offcampus] 02/14: Deep Learning and RNA structure -- Bing Bing; Ruzzo Christoph Flamm, Julia Wielach, Michael T. Wolfinger, Stefan Badelt, Ronny Lorenz, and Ivo L. Hofacker. "Caveats to deep learning approaches to RNA secondary structure prediction." https://www.biorxiv.org/content/10.1101/2021.12.14.472648v1 02/21:   -- Holiday 02/28: Unsupervised Transformers Learn Protein Structures -- Pascal; Wang Roshan Rao, Joshua Meier, Tom Sercu, Sergey Ovchinnikov, Alexander Rives, "Transformer protein language models are unsupervised structure learners." https://openreview.net/forum?id=fylclEqgvgd 03/07: Protein Fitness -- Alyssa C Hsu, H Nisonoff, C Fannjiang, J Listgarten, "Learning protein fitness models from evolutionary and assay-labeled data." Nat Biotechnol, (2022) . [offcampus]
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 L Zappia, FJ Theis, "Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape." Genome Biol, 22, #1 (2021) 301. [offcampus] Wouter suggested the following review paper I Jerkovic, G Cavalli, "Understanding 3D genome organization by multidisciplinary methods." Nat Rev Mol Cell Biol, 22, #8 (2021) 511-528. [offcampus] 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 bioinformatics.org, 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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