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  CSE 590CAu '14:  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, EE1 026 (schematic)
Organizers:  Joe Felsenstein, Su-In Lee, Bill Noble, Larry Ruzzo, Cole Trapnell
Credit: 1-3 Variable
Grading: Credit/No Credit. Talk to the organizers if you are unsure of our expectations.
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 Date  Presenters/Participants Topic Details
09/29---- Organizational Meeting ----
10/06Jacob; LeeCell Types from Single-Cell ExpressionDetails
10/13Antoine, Scott; LeeModeling Chromatin Factor InteractionsDetails
10/20Jiechen; LeeCombining Clinical and Expression Data in Breast CancerDetails
10/27No Class: Instead, check out the Statistics Seminar.
11/03Katie; NoblePeptide Mixture SpectraDetails
11/10No Class: Instead, check out the Genome Sciences Symposium.
11/17Safiye; RuzzoRNA Dynamics From Single RNAseq SamplesDetails
11/24Nao; RuzzoConserved RNA Structures in GenomesDetails
12/01Daniel; TrapnellModeling Bi-modality in Single-Cell Gene ExpressionDetails
12/08Alex, Max; Trapnell(NEW ROOM: CSE 403) Gene Pair Signatures of Lineage ControlDetails

 Papers, etc.

  Note on Electronic Access to Journals

Links to full papers below are often to journals that require a paid subscription. The UW Library is generally a paid subscriber, and you can freely access these articles if you do so from an on-campus computer. 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 once per session.  

09/29: ---- Organizational Meeting ----

10/06: Cell Types from Single-Cell Expression -- Jacob; Lee

10/13: Modeling Chromatin Factor Interactions -- Antoine, Scott; Lee

10/20: Combining Clinical and Expression Data in Breast Cancer -- Jiechen; Lee

10/27:   -- No Class: Instead, check out the Statistics Seminar.

11/03: Peptide Mixture Spectra -- Katie; Noble

11/10:   -- No Class: Instead, check out the Genome Sciences Symposium.

11/17: RNA Dynamics From Single RNAseq Samples -- Safiye; Ruzzo

  • JM Gray, DA Harmin, SA Boswell, N Cloonan, TE Mullen, JJ Ling, N Miller, S Kuersten, YC Ma, SA McCarroll, SM Grimmond, M Springer, "SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample." PLoS ONE, 9, #2 (2014) e89673. [offcampus]

11/24: Conserved RNA Structures in Genomes -- Nao; Ruzzo

12/01: Modeling Bi-modality in Single-Cell Gene Expression -- Daniel; Trapnell

12/08: (NEW ROOM: CSE 403) Gene Pair Signatures of Lineage Control -- Alex, Max; Trapnell

  • M Heinäniemi, M Nykter, R Kramer, A Wienecke-Baldacchino, L Sinkkonen, JX Zhou, R Kreisberg, SA Kauffman, S Huang, I Shmulevich, "Gene-pair expression signatures reveal lineage control." Nat. Methods, 10, #6 (2013) 577-83. [offcampus]

 Other  Seminars Past quarters of CSE 590C
COMBI & Genome Sciences Seminars
Biostatistics Seminars
Microbiology Department Seminars

 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 very comprehensive FAQ at, including annotated references 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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