| Course Info |
|
Reading and Research in Computational Biology
Mondays, 3:30-5:00, 003 EE1
CSE 590 CB is an informal weekly seminar in Computational
Biology, open to all graduate students in the computer,
biological, and mathematical sciences.
| Instructors: |
Karp,
Ruzzo,
Tompa
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| Credit: |
1-3 Variable |
| Grading: |
Credit/No Credit. Talk to instructors if
you're unsure about our expectations, registrar-wise.
|
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| Email/Bboard
| Email/Bboard
Log
(All mail to the seminar e-mail list,
cse590cb@cs.
Last:
06/17/99, 11PM.)
|
| Schedule |
| Date |
Topic |
Presenters (Faculty Consultant) |
Papers |
 |
| 3/29 |
Organizational Meeting | | |
| 4/05 |
Regulation I: The Manifesto | Jeremy Buhler |
RegI |
| 4/12 |
SBH |
Kerry Bubb, Agatha Liu (Karp) |
Misc 1
|
| 4/19 |
Regulation II: Mutual Information |
Agatha Liu, Nitin Sharma, Saurabh Sinha, Ken Yasuhara (Ruzzo) |
RegII
|
| 4/26 |
Genetic Linkage Analysis |
Dan Geiger (Microsoft & Technion) |
Linkage |
| 5/3 |
Guest Speaker |
Carol Sibley |
|
| 5/10 |
Guest Speaker |
Garrett Odell |
|
| 5/17 |
Guest Speaker |
Carol Sibley |
|
| 5/24 |
Guest Speaker |
Stan Fields |
|
| 5/31 |
Holiday |
|
|
| 6/7 |
Finals Week; No Meeting?? |
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| Papers |
Miscellaneous
- A. Freize, F. Preparata, and E. Upfal,
"Optimal Reconstruction of a Sequence From its Probes,"
unpubl.
Regulation I: General
- J. Buhler, "Modeling Regulatory
Networks: a Manifesto", unpubl., 1999.
http://www.cs.washington.edu/homes/jbuhler/manifesto.ps
Regulation II: Mutual Information
- S.Liang, S. Fuhrman, R. Somogyi, "REVEAL:
A General Reverse Engg. Algorithm for Inference of Genetic
Network Architectures", Pacific Symposium on BioComputing
3:18-29 (1998).
http://www-smi.stanford.edu/projects/helix/psb98/liang.pdf
- T. Akutsu, S. Miyano, S. Kuhara,
"Identification of Genetic Networks from Small Number of
Gene Expression Patterns Under the Boolean Network Model",
Pac. Sym. Bio. 4:17-28 (1999).
http://www-smi.stanford.edu/projects/helix/psb99/Akutsu.pdf
Regulation III. Neural Networks (weight matrix)
4/19-5/3. Mathieu Blanchette, Jeremy Buhler, Agatha Liu (Rimli
Sengupta, Martin Tompa)
- D. C. Weaver, C. T. Workman, G. D. Stormo, "Modeling
Regulatory Networks with Weight Matrices", Pac. Sym. Bio.
4:112-123 (1999).
http://www-smi.stanford.edu/projects/helix/psb99/Weaver.pdf
- P. D'Haeseleer, X. Wen, S. Furhman, R. Somogyi, "Linear
Modeling of mRNA Expression Levels During CNS Development
and Injury", Pac. Sym. Bio. 4:41-52 (1999).
http://www-smi.stanford.edu/projects/helix/psb99/Dhaeseleer.pdf
Regulation IV. Dynamical Systems
5/3-5/17. Matt Carey, Dan Fasulo, Trey Ideker (Rimli Sengupta,
Martin Tompa)
- R. Thomas, D. Thieffry, M. Kauffman, "Dynamical Behavior
of Biological Regulatory Networks -- I. Biological role of
feedback loops and practical use of the concept of
loop-characteristic state", Bull. Math. Biol. 57:247-76
(1995).
- D. Thieffry, R. Thomas, "Dynamical Behavior of Biological
Regulatory Networks -- II. Immunity control in phage
lambda", Bull. Math. Biol. 57:277-97 (1995).
- A. Wuensche, "Genomic Regulation Modeled as a Network
with Basins of Attraction", Pac. Sym. Bio 3:89-102 (1998).
http://www-smi.stanford.edu/projects/helix/psb98/wuensche.pdf
- D. Thieffry, R. Thomas, "Qualitative Analysis of
Gene Networks", Pac. Sym. Bio. 3:77-88 (1998).
http://www-smi.stanford.edu/projects/helix/psb98/thieffry.pdf
Regulation V. Empirical
5/17-5/31. Stephen Ramsey, Wendy Thomas, Ka Yee Yeung (Rimli
Sengupta, Martin Tompa)
- C-H. Yuh, J. G. Moore, E. H. Davidson, "Quantitative
Functional Interrelations Within the Cis-regulatory System
of the S. Purpuratus Endo16 Gene", Development
122:4045-4056 (1996).
http://www.biologists.com/Development/122/12/dev5095.html
- C-H. Yuh, E. H. Davidson, "Modular Cis-regulatory
Organization of Endo16, a Gut-specific Gene of the Sea
Urchin Embryo", Development 122:1069-1082 (1996).
http://www.biologists.com/Development/122/04/dev5052.html
Below are suggested papers for the two pots that we didn't have
time to cover this quarter.
Regulation VI. Stochastic
- A. Arkin, J. Ross, H. H. McAdams, "Stochastic Kinetic
Analysis of Developmental Pathway Bifurcation in Phage
Lambda-Infected E. Coli Cells", Genetics 149:1633-48
(1998).
- D. T. Gillespie, "A General Method for Numerically
Simulating the Stochastic Time Evolution of Coupled Chemical
Reactions", J. Comput. Phy. 22:403-34 (1976).
- M. Gibson, J. Bruck, "An Efficient Algo. for Generating
Trajectories of Stochastic Gene Regulation Reactions", Tech.
Report. ETR026 , Dept. of Computation and Neural Systems,
CalTech (1998).
http://www.paradise.caltech.edu/papers/etr026.ps
Regulation VII. Discrete Algorithms
- T. Chen, V. Filkov, S. Skiena, "Identifying Gene
Regulatory Networks from Experimental Data", Recomb (1999).
- T. Akutsu, S. Kuhara, O. Maruyama, S. Miyano,
"Identification of Gene Regulatory Networks by Strategic
Gene Disruptions and Overexpressions", ACM Symposium on
Discrete Algorithms (SODA), 1998.
Genetic Linkage Analysis
- Kenneth Lang, Mathematical and Statistical methods for
Genetic Analysis, Springer, 1997.
Dan says: "A good introduction well suited for computer
scientists. I will use some material from Chapters 1 and 7
which are quite self contained."
- Lander and Green, Construction of multilocus genetic
linkage maps in humans. Proc. Natl. Acad. Sci. USA, Vol 84,
pp. 2363-2367, April 1987.
- Kruglyak et al. Parametric and Non parametric Linkage
Analysis: A unified Multipoint Approach. Am J. Hum. Genet.
(1996), 58:1347-1363.
- Elizabeth Thompson, Monte Carlo Likelihood in Genetic
Mapping. Statistical Science, 1994, Vol 9., No 3, 355-366.
- O'Connell and Weeks, The VITESSE algorithm for rapid
exact multilocus linkage analysis via genotype set-recording
and fuzzy inheritance. Nature Genetics, Vol 11, December
1995, pp. 402--408.
- Becker, Geiger, Schaffer, Automatic Selection of Loop
Breakers for Genetic Linkage Analysis, Human Heredity
48:49--60, 1998.
|
| Resources |
CSE 590 CB, Winter, 1999.
CSE 590 CB, Autumn, 1998.
Lecture notes from the two offerings
of CSE 590 BI (Computational Biology).
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