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 CSE 590 CB, Spring 1999
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 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
Credit: 1-3 Variable
Grading: Credit/No Credit. Talk to instructors if you're unsure about our expectations, registrar-wise.

 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??    

 Papers

Miscellaneous

  1. A. Freize, F. Preparata, and E. Upfal, "Optimal Reconstruction of a Sequence From its Probes," unpubl.

Regulation I: General

  1. J. Buhler, "Modeling Regulatory Networks: a Manifesto", unpubl., 1999.
    http://www.cs.washington.edu/homes/jbuhler/manifesto.ps

Regulation II: Mutual Information

  1. 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
  2. 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)
  1. 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
  2. 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)
  1. 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).

  2. D. Thieffry, R. Thomas, "Dynamical Behavior of Biological Regulatory Networks -- II. Immunity control in phage lambda", Bull. Math. Biol. 57:277-97 (1995).

  3. 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
  4. 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)
  1. 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
  2. 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

  1. 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).

  2. D. T. Gillespie, "A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions", J. Comput. Phy. 22:403-34 (1976).

  3. 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

  1. T. Chen, V. Filkov, S. Skiena, "Identifying Gene Regulatory Networks from Experimental Data", Recomb (1999).

  2. 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

  1. 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."

  2. Lander and Green, Construction of multilocus genetic linkage maps in humans. Proc. Natl. Acad. Sci. USA, Vol 84, pp. 2363-2367, April 1987.

  3. Kruglyak et al. Parametric and Non parametric Linkage Analysis: A unified Multipoint Approach. Am J. Hum. Genet. (1996), 58:1347-1363.

  4. Elizabeth Thompson, Monte Carlo Likelihood in Genetic Mapping. Statistical Science, 1994, Vol 9., No 3, 355-366.

  5. 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.

  6. 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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