Some possible papers for project

• Network Motifs: Simple Building Blocks of Complex Networks, R Milo, S Shen-Orr, S Itzkovitz, N Kashtan, D Chklovskii & U Alon, Science, 298:824-827 (2002).
• Construction of a genetic toggle switch in Escherichia coli, Nature 403, 339 - 342 (2000) Timothy S. Gardner, Charles R. Cantor, James J. Collins
• Synchronizing genetic relaxation oscillators by intercell signaling, Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):679-84. McMillen D, Kopell N, Hasty J, Collins JJ.
• Essential nonlinearities in hearing, Eguiluz, V. M., Ospeck, M., Choe, Y., Hudspeth, A. J. & Magnasco, M. O. Physical Review Letters 84, 5232-5235 (2000).
• Prediction and measurement of an autoregulatory genetic module, Isaacs FJ, Hasty J, Cantor CR, Collins JJ., Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7714-9.
• Multistationarity, the Basis of Cell Differentiation and Memory. I. Structural Conditions of Multistationarity and Other Non-Trivial Behaviour, R. Thomas and M. Kaufman Chaos 11,170-179 (2001).
• MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network, Bhalla US, Ram PT, Iyengar R., Science. 2002 Aug 9;297(5583):948-9.
• Dynamic behavior in mathematical models of the tryptophan operon, Moises Santillan and Michael C. Mackey Chaos: An Interdisciplinary Journal of Nonlinear Science Vol 11(1) pp. 261-268. March 2001
• Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices, Famili I, Palsson BO, J Theor Biol. 2003 Sep 7;224(1):87-96.
• Frequency domain analysis of noise in autoregulated gene circuits, Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4551-6. Simpson ML, Cox CD, Sayler GS.
• A Model of Periodic Oscillation for Genetic Regulatory Systems, IEEE Transactions On Circuits And Systems I: Fundamental Theory And Applications, VOL. 49, NO. 10, October 2002 1429 Luonan Chen and Kazuyuki Aihara
• Using mathematics to understand HIV immune dynamics, Kirschner D. AMS Notices pp. 191-202, February 1996. (This paper is a bit older than the rest, and quite different. But since there was a talk about the subject in class, some of you might be interested.)
• Network Dynamics And Cell Physiology, Nat Rev Mol Cell Biol. 2001 Dec;2(12):908-16. Tyson JJ, Chen K, Novak B. (This paper is more of a "survey" and expository type.)