| 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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| Schedule |
| Date |
Presenters/Participants |
Topic |
Details |
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| 10/03 | ---- Organizational Meeting ---- |
|---|
| 10/10 | Daniel; Tompa | Primate exome sequencing | Details |
|---|
| 10/17 | Miles; Ruzzo | Non-coding variation | Details |
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| 10/24 | Elizabeth; Noble | Selection and nucleosome positioning | Details |
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| 10/31 | Michael; Felsenstein | Network Archaeology | Details |
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| 11/07 | Sam; Tompa | miRNA targets in repetitive coding sequence | Details |
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| 11/14 | Ajit; Ruzzo | Gibbs sampling for RNA prediction | Details |
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| 11/21 | Dr. Jesse Bloom, FHCRC | The role of epistasis in protein and viral evolution | |
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| 11/28 | Max; Noble | More on nucleosome positioning | Details |
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| 12/05 | John; Borenstein | Simplicity in metabolic networks | Details |
|---|
Fall schedule is now filled. FYI, here are the other papers that were suggested.
Borenstein (both; one is a short revew of the other): - JA Bachman, P Sorger, "New approaches to modeling complex biochemistry." Nat. Methods, 8, #2 (2011) 130-1.
[offcampus]
- MW Sneddon, JR Faeder, T Emonet, "Efficient modeling, simulation and coarse-graining of biological complexity with NFsim." Nat. Methods, 8, #2 (2011) 177-83.
[offcampus]
Felsenstein (either or both): - S Navlakha, C Kingsford, "Network archaeology: uncovering ancient networks from present-day interactions." PLoS Comput. Biol., 7, #4 (2011) e1001119.
[offcampus]
- D Xie, CC Chen, X He, X Cao, S Zhong, "Towards an evolutionary model of transcription networks." PLoS Comput. Biol., 7, #6 (2011) e1002064.
[offcampus]
Noble (another on nucleosome (re-)positioning).
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| 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.
10/03: ---- Organizational Meeting ----
10/10: Primate exome sequencing -- Daniel; Tompa
- RD George, G McVicker, R Diederich, SB Ng, AP Mackenzie, WJ Swanson, J Shendure, JH Thomas, "Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection." Genome Res, 21, #10 (2011) 1686-1694.
[offcampus]
10/17: Non-coding variation -- Miles; Ruzzo
10/24: Selection and nucleosome positioning -- Elizabeth; Noble
- JG Prendergast, CA Semple, "Widespread signatures of recent selection linked to nucleosome positioning in the human lineage." Genome Res, (2011) .
[offcampus]
10/31: Network Archaeology -- Michael; Felsenstein
11/07: miRNA targets in repetitive coding sequence -- Sam; Tompa
11/14: Gibbs sampling for RNA prediction -- Ajit; Ruzzo
11/21: The role of epistasis in protein and viral evolution -- Dr. Jesse Bloom, FHCRC
11/28: More on nucleosome positioning -- Max; Noble
One or both of - A Tsankov, Y Yanagisawa, N Rhind, A Regev, OJ Rando, "Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization." Genome Res, (2011) .
[offcampus]
- JB Zaugg, NM Luscombe, "A genomic model of condition-specific nucleosome behaviour explains transcriptional activity in yeast." Genome Res, (2011) .
[offcampus]
12/05: Simplicity in metabolic networks -- John; Borenstein
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