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  CSE 590CSp '11:  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, EEB 031 (schematic)
Organizers:  Elhanan Borenstein, Joe Felsenstein, Hamid Bolouri, Bill Noble, Su-In Lee, Larry Ruzzo, Martin Tompa
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
03/28---- Organizational Meeting ----
04/04Xinxia Peng, MicrobiologymRNA-seq normalization 
04/11Hamid Bolouri, FHCRCNetwork modeling to get more out of high throughput screening data 
04/18Elizabeth Tseng & Daniel Jones, CSETwo Short TalksDetails
04/25Indika Rajapakse, FHCRCMapping the dynamic relationship between the nuclear spatial network and functionDetails
05/02Julia Palacios, StatisticsEffective population size under the coalescent 
05/09The Fifth CMB Spring Symposium, 1:00-5:30, CSE 691
05/16Sharon Greenblum & Roie Levy, Genome SciencesOpen computational problems in microbiome research 
05/23Benjamin Diament, CSEProgress in Nimble Peptide Identification Software 

 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.  

03/28: ---- Organizational Meeting ----

04/04: mRNA-seq normalization -- Xinxia Peng, Microbiology

04/11: Network modeling to get more out of high throughput screening data -- Hamid Bolouri, FHCRC

04/18: Two Short Talks -- Elizabeth Tseng & Daniel Jones, CSE

  • Tseng: A cost-effective method for characterizing bacterial communities using high-throughput sequencing
  • Jones: Correcting for bias in high-throughput sequencing data

04/25: Mapping the dynamic relationship between the nuclear spatial network and function -- Indika Rajapakse, FHCRC

   Abstract:   Genomes are complex physical structures, and their dynamic functional output-time dependent gene expression-is related to spatial organization as well as local chromatin status. We seek to define a general framework for mapping the dynamic relationship between one-dimensional features, such as patterns of histone modifications, transcription profiles and replication profiles, and 3D genome architecture constructed from integration of Hi-C (genome conformation capture) and single cell interphase 3D-FISH (fluorescent in situ hybridization). This dynamic relationship may give insight into the process of cellular differentiation. Typically, constructed biological networks exist in an abstract space, where the positions of the network nodes are not considered. We argue that geography matters greatly for network function, and the nodes (genes) occupy particular positions in space and reconfigure over time. To facilitate 3D analyses, we are developing an automated computational tool for characterizing the spatial architecture of the nucleus in a single cell. I will use an example from our data to demonstrate this analysis.

Joint work with: Mark Groudine (FHCRC), David Scalzo (FHCRC), Michael Perlman (Statistics, UW), and John Snyder (Microsoft Research).

Suggested reading:

  • E Lieberman-Aiden, NL van Berkum, L Williams, M Imakaev, T Ragoczy, A Telling, I Amit, BR Lajoie, PJ Sabo, MO Dorschner, R Sandstrom, B Bernstein, MA Bender, M Groudine, A Gnirke, et 4 al., "Comprehensive mapping of long-range interactions reveals folding principles of the human genome." Science, 326, #5950 (2009) 289-93. [offcampus]

05/02: Effective population size under the coalescent -- Julia Palacios, Statistics

05/09:   -- The Fifth CMB Spring Symposium, 1:00-5:30, CSE 691

See link for details. The subsumes CSE 590C this week.

05/16: Open computational problems in microbiome research -- Sharon Greenblum & Roie Levy, Genome Sciences

05/23: Progress in Nimble Peptide Identification Software -- Benjamin Diament, CSE

05/30:   -- Holiday

 Other  Seminars Past quarters of CSE 590C
COMBI & Genome Sciences Seminars
Applied Math Department Mathematical Biology Journal Club
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
CSE 590TV/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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University of Washington
Box 352350
Seattle, WA  98195-2350
(206) 543-1695 voice, (206) 543-2969 FAX