Course Info |
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CSE 590C is a weekly seminar on Readings and Research in Computational Biology, open to all
graduate students in computational, biological, and mathematical sciences.
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Email |
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Theme |
This quarter's discussion will focus (loosely) on single-cell -omics and multi-omic integration. See
suggested papers below, or propose another one. |
Schedule |
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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.
01/04: -- ---- Organizational Meeting ----
01/11: Overview of Single Cell Omics -- Ayse; Larry
Suggested reading:
Other reviews, if you want more:
- QR Xing, NO Cipta, K Hamashima, YC Liou, CG Koh, YH Loh, "Unraveling Heterogeneity in Transcriptome and Its Regulation Through Single-Cell Multi-Omics Technologies." Front Genet, 11, (2020) 662.
[offcampus]
01/18: -- Holiday
01/25: Biologically Interpretable Deep Learning On Single-Cell Data -- Lee, Ethan; Larry
02/01: SC Integration with Transfer Learning -- Ashley, Addie; Sheng
02/08: Benchmarking SC Network Inference Methods -- Johannes, Aji; Yuliang
02/15: -- Holiday
02/22: -- No Class: Instead, check out the CSE colloquium, Zoom link here.
03/01: Sequence Motif Learning & Representation -- Erin; Larry
03/08: -- No Class
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Other Papers |
Other suggested topics/papers: See suggested papers below, or
propose another one. (Contact ruzzo at uw.edu.)
- Bill suggests:
- Y Baran, A Bercovich, A Sebe-Pedros, Y Lubling, A Giladi, E Chomsky, Z Meir, M Hoichman, A Lifshitz, A Tanay, "MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions." Genome Biol, 20, #1 (2019) 206.
[offcampus]
- Ayse suggests:
- R Argelaguet, B Velten, D Arnol, S Dietrich, T Zenz, JC Marioni, F Buettner, W Huber, O Stegle, "Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets." Mol Syst Biol, 14, #6 (2018) e8124.
[offcampus]
- Su-In suggests an image genomics paper:
- B He, L Bergenstråhle, L Stenbeck, A Abid, A Andersson, Å Borg, J Maaskola, J Lundeberg, J Zou, "Integrating spatial gene expression and breast tumour morphology via deep learning." Nat Biomed Eng, 4, #8 (2020) 827-834.
[offcampus]
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Other Seminars |
Past quarters of CSE 590C
COMBI & Genome Sciences Seminars
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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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