CAAM/STAT 499, BioMath Foundations Seminar, Spring 2004
Modeling and Simulation of Genetic Regulatory Systems
When & Where: Wednesdays 5-6 PM in HUM 117
Resources: Human
Blair Christian, blairc@rice.edu
Steve Cox, cox@rice.edu
Mark Embree, embree@rice.edu
Rudy Guerra, rguerra@rice.edu
Brad Peercy, bpeercy@rice.edu
Resources: 2 monographs, a review paper, a hypertext and a site
[1] M. Ptashne and A. Gann, Genes & Signals, Cold Spring Harbor
Laboratory Press, 2002.
[2] P. Baldi and G.W. Hatfield, DNA Microarrays and Gene Expression:
From Experiments to Data Analysis and Modeling, Cambridge University Press,
2002.
[3] H. De Jong, Modeling and Simulation of Genetic Regulatory Systems:
A Literature Review, Journal of Computational Biology, Vol. 9, No. 1, 2002,
pp. 67-103.
[4]
Biology Hypertext.
[5]
BIOC 4103 in Newfoundland
There are a large number of beautiful/intriguing/maddening introductory/expository texts. Some favorites are
[A] E. Schroedinger, What is Life?
[B] A. Kornberg, For the Love of Enzymes: The Odyssey of a Biochemist.
[C] J.D. Watson (and G.S. Stent), The Double Helix, Norton Critical Edition.
[D] R. Dawkins, The Selfish Gene.
[E] S. Kauffman, The Origins of Order.
Schedule:
January 14: Organizational Meeting.
Reading for next week: chapter 7 of [4] and sections 1-4 of [3].
January 21: [1] Chapter 1, Lessons From Bacteria: The Lac Operon and Bacteriophage lambda. Also hit chapter 7 of [4] and
here . You may also wish to preview the circuit diagram of
McAdams & Shapiro .
January 28: [3, sec. 4], Boolean Networks. Origins: S. Kauffman, The Large
Scale Structure and Dynamics of Gene Control Circuits, J. Theoretical Biology
44, 1974, pp. 167-190.
Tutorial
and Phage Example and an Inference Paper
Februry 4: [3 sec.6], Nonlinear Ordinary Differential Equations.
We follow Chapter 9 in Computational Cell Biology, Fall, Maryland, Wagnerand Tyson, eds., Springer, 2002.
Februry 11: [3 sec. 10], Stochastic Simulation. Its application to
chemical reactions stems from work of
Gillespie. We have coded two of his examples.
This code produced this
plot and
this code produced this
plot.
See Arkin et al. for its application to Phage lambda.
StochSim
is a general purpose biochemical simulator.
February 18: [2] Chapter 4, Gene Expression Profiling Experiments.
Also, check out Chapters 3 & 4 of
Microarray Gene Expression Data Analysis: A beginners guide
(ISBN 1-4051-0682-4, Blackwell Publishing)
February 25: [2] Chapters 5 and 6, Statistical Analysis of Array Data
March 10: The role of Oxygen. Brad Peercy.
March 17: Neuronal Calcium Signaling. Steve Cox.
March 24: Phage &lambda. Jay Raol
March 31: Probabilistic Boolean Nets. Ed Castillo
April 7: Reverse Engineering
April 14: Meta and Neuro Updates
April 21: The Game of Life
Work:
1 credit: Participate in Wednesday seminar meetings and complete
two writing assignments.
2 credits: Take an active role in a
PFUG and complete
two writing assignments.
3 credits: Take an active role in a
PFUG and complete
four writing assignments.
To complete a writing assignment is to submit (at least) two type written,
1-inch margin, double-spaced, 12pt font pages that review a relevant
lecture, paper or text.