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,
Steve Cox,
Mark Embree,
Rudy Guerra,
Brad Peercy,

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.


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


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.