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CSE 590C, Sp '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.
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| Schedule |
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| Papers, etc. |
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.
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| 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:
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"
CSE's Computational Molecular Biology research group
Interdisciplinary Ph.D. program in Computational Molecular Biology
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Computer Science & Engineering University of Washington Box 352350 Seattle, WA 98195-2350 (206) 543-1695 voice, (206) 543-2969 FAX |
Note on Electronic Access to Journals