Stochastic Dynamics of Gene Expression

1. Theories of Gene Switches and Networks

On and off of gene switches are controlled by binding of regulatory proteins such as repressors or activators to DNA. These regulatory proteins are produced by other genes, so that those genes form the network of regulations. How do such networks process information and how are they designed ? Here, we should note that constituent molecules of these networks, DNA, mRNA and regulatory proteins, are small in their numbers in a cell. Due to the smallness of numbers of these molecules, intense stochastic fluctuations are inevitable in each cell, which generates cell-to-cell variation in a genetically identical population of cells. We develop mathematical theories of stochastic gene expression and simulate those noisy o processes to analyze the design principle of networks.
M. Sasai & P.G. Wolynes, "Stochastic Gene Expression as a Many Body Problem", Proc. Natl. Acad. Sci. USA 100(5) 2374-2379 (2003).
M. Yoda, T. Ushikubo, W. Inoue & M. Sasai, "Roles of noise in single and coupled multiple genetic oscillators", J. Chem. Phys. 126(11) 115101-1-11 (2007).
Y. Okabe, Y. Yagi & M. Sasai, "Effects of the DNA state fluctuation on single-cell dynamics of self-regulating gene", J. Chem. Phys. 127, 105107 (2007).
Y. Okabe & M. Sasai. "Stable stochastic dynamics in yeast cell cycle", Biophysical J. 93, 3451-3459 (2007).

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