| 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 on both single-cell "omics" and nanopore sequencing. |
| Schedule |
| Date |
Presenters/Participants |
Topic |
Details |
 | | 01/09 | ---- Organizational Meeting ---- |
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| 01/16 | Holiday |
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| 01/23 | Sudipto, Shunfu; Kannan | Single cell 1 | Details |
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| 01/30 | Jack; Kannan | Single cell 2 | Details |
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| 02/06 | ---- Canceled; Snow Day! ---- |
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| 02/13 | Safiye, Katie, Nao; Kannan | Single cell 3 | Details |
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| 02/20 | Holiday |
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| 02/27 | Eliah; Ruzzo | Nanopore 1 | Details |
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| 03/06 | Jacob; Ruzzo | Nanopore 2 | Details |
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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.
01/09: -- ---- Organizational Meeting ----
01/16: -- Holiday
01/23: Single cell 1 -- Sudipto, Shunfu; Kannan
Learning
dynamics and transcriptional network structure from single cell sequenced data.
01/30: Single cell 2 -- Jack; Kannan
- M Setty, MD Tadmor, S Reich-Zeliger, O Angel, TM Salame, P Kathail, K Choi, S Bendall, N Friedman, D Pe'er, "Wishbone identifies bifurcating developmental trajectories from single-cell data." Nat. Biotechnol., 34, #6 (2016) 637-45.
[offcampus]
02/06: -- ---- Canceled; Snow Day! ----
02/13: Single cell 3 -- Safiye, Katie, Nao; Kannan
- A Dixit, O Parnas, B Li, J Chen, CP Fulco, L Jerby-Arnon, ND Marjanovic, D Dionne, T Burks, R Raychowdhury, B Adamson, TM Norman, ES Lander, JS Weissman, N Friedman, et 1 al., "Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens." Cell, 167, #7 (2016) 1853-1866.e17.
[offcampus]
02/20: -- Holiday
02/27: Nanopore 1 -- Eliah; Ruzzo
03/06: Nanopore 2 -- Jacob; Ruzzo
- J Schreiber, ZL Wescoe, R Abu-Shumays, JT Vivian, B Baatar, K Karplus, M Akeson, "Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands." Proc. Natl. Acad. Sci. U.S.A., 110, #47 (2013) 18910-5.
[offcampus]
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| Other Papers |
Other suggested topics/papers that didn't fit the schedule:
- Multi-omic data analysis; Molecular understanding of different cell types using omic data (roughly)
- A review paper on multi-omics:
Brief argument for/against this paper: Since it is
a review paper, it covers the intuition behind the various methods more than the detail of each. This could
be a nice way to open the quarter, but it definitely lacks some computational depth.
- A paper covering a multi-outcome GWAS on insulin resistance.
- LA Lotta, P Gulati, FR Day, F Payne, H Ongen, M van de Bunt, KJ Gaulton, JD Eicher, SJ Sharp, J Luan, E De Lucia Rolfe, ID Stewart, E Wheeler, SM Willems, C Adams, et 17 al., "Integrative genomic analysis implicates limited peripheral adipose storage capacity in the pathogenesis of human insulin resistance." Nat. Genet., 49, #1 (2017) 17-26.
[offcampus]
Pros: Rather than check association with a single outcome, this paper does GWAS against multiple phenotypes
as a surrogate for a more invasive phenotype. They seem to followup the association study with interesting
results that demonstrate how to followup on SNPs to get mechanistic insight.
Cons: I have not delved into the math yet so I don't know how interesting it will be.
- An interesting paper presenting an integrative analysis showing that disease-associated
GWAS variants perturb tissue-specific regulatory modules:
- Deep learning applications in computational biology:
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| Other Seminars |
Past quarters of CSE 590C
COMBI & Genome Sciences Seminars
Biostatistics Seminars
Microbiology Department Seminars
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| 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 bioinformatics.org, 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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