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  CSE 590CSp '09:  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:  Joe Felsenstein, Bill Noble, 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
03/30---- Organizational Meeting ----
04/06Xinxia Peng, MicrobiologyComputational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human liversDetails
04/13Max Robinson, GSmiRNA TargetsDetails
04/20Elizabeth Tseng, CSEFinding ncRNA in bacteria 
04/27Martin Tompa, Elizabeth Tseng, CSEFinding extremely constrained sequences 
05/04Michael Hoffman, GSSegway: a dynamic Bayesian network for genomic segmentationDetails
05/11Zafer Aydin, GSA dynamic Bayesian network approach for protein secondary structure prediction 
05/18Stefan Seemann, CopenhagenncRNAs in mouse brain 
06/01CMB Annual SymposiumPlease join us in CSE 691, 1-5 pmDetails

 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.  

03/30: ---- Organizational Meeting ----

04/06: Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers -- Xinxia Peng, Microbiology

   Abstract:   Hepatitis C virus (HCV) is a major cause of chronic liver disease by infecting over 170 million people worldwide. Recent studies have shown that microRNAs (miRNAs), a class of small non-coding regulatory RNAs, are involved in the regulation of HCV infection, but their functions have not been systematically studied. We propose an integrative strategy for identifying the miRNA-mRNA regulatory modules that are associated with HCV infection. This strategy combines paired expression profiles of miRNAs and mRNAs and computational target predictions. A miRNA-mRNA regulatory module consists of a set of miRNAs and their targets, in which the miRNAs are predicted to coordinately regulate the level of the target mRNA.

We simultaneously profiled the expression of cellular miRNAs and mRNAs across 30 HCV positive or negative human liver biopsy samples using microarray technology. We constructed a miRNA-mRNA regulatory network, and using a graph theoretical approach, identified 38 miRNA-mRNA regulatory modules in the network that were associated with HCV infection. We evaluated the direct miRNA regulation of the mRNA levels of targets in regulatory modules using previously published miRNA transfection data. We analyzed the functional roles of individual modules at the systems level by integrating a large-scale protein interaction network. We found that various biological processes, including some HCV infection related canonical pathways, were regulated at the miRNA level during HCV infection.

Our regulatory modules provide a framework for future experimental analyses. This report demonstrates the utility of our approach to obtain new insights into post-transcriptional gene regulation at the miRNA level in complex human diseases.

04/13: miRNA Targets -- Max Robinson, GS

04/20: Finding ncRNA in bacteria -- Elizabeth Tseng, CSE

04/27: Finding extremely constrained sequences -- Martin Tompa, Elizabeth Tseng, CSE

05/04: Segway: a dynamic Bayesian network for genomic segmentation -- Michael Hoffman, GS

      Some background reading:

  • ENCODE Project Consortium, E Birney, JA Stamatoyannopoulos, A Dutta, R Guigó, et 314 al., "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project." Nature, 447, #7146 (2007) 799-816. [offcampus]
  • Bilmes JA, Bartels C. "Graphical model architectures for speech recognition." IEEE Signal Proc Mag 22:89. pdf.

05/11: A dynamic Bayesian network approach for protein secondary structure prediction -- Zafer Aydin, GS

05/18: ncRNAs in mouse brain -- Stefan Seemann, Copenhagen

05/25:   -- Holiday

06/01: Please join us in CSE 691, 1-5 pm -- CMB Annual Symposium

Please join us for the annual Computational Molecular Biology spring symposium!

Date: Monday, June 1
Time: 1:00 - 5:00 pm
Room: CSE 691, "Gates Commons" building location

1:00 Cindy Desmarais, Genome Sciences,
Certificate Presentation: "Comparing polymorphism and divergence in resequenced human genes using the HKA framework"

1:30 Elizabeth Tseng, Computer Science and Engineering,
"Finding non-coding RNAs in bacteria through a quasi-clique-finding algorithm"

2:00 Chester Ni, Microbiology,
"Systems biology approaches in virus-host interaction research -- computational opportunities and challenges"

2:30: Kavita Garg, Fred Hutchinson Cancer Research Center:
"Computational analysis of microRNA regulation with application to ovarian cancer"

3:00: Break

3:30: Hong Qian, Applied Mathematics,
"Cellular dynamics from a computational chemistry perspective"

4:00: Bill Noble, Genome Sciences,
"Several problems that arise in the analysis of shotgun proteomics tandem mass spectral data sets"

4:30: Phil Bradley, Fred Hutchinson Cancer Research Center:
"Structure-based prediction of protein-DNA interactions"

 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.
S-Star Bioinformatics Online Course Schedule, a collection of video primers
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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Seattle, WA  98195-2350
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