Publications Systems Biology

Ahmed, T., Shimizu, T. S., Stocker, R. (2010). Microfluidics for bacterial chemotaxis. Integrative Biology In press.

Ahmed, T., Shimizu, T. S., Stocker, R. (2010). Bacterial chemotaxis in linear and nonlinear steady microfluidic gradients. Nano Letters In press.

Shimizu, T. S., Tu, Y. & Berg, H. C. (2010). A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli. Mol Syst Biol 6:382.

Tu, Y., Shimizu, T. S. & Berg, H. C. (2008). Modeling the chemotactic response of Escherichia coli to time-varying stimuli. PNAS 105:14855-14860.

Shimizu, T. S., Le Novère, N. (2008). Looking inside the box: bacterial transistor arrays. Mol Microbiol 69:5-9.

Sourjik, V., Vaknin, A., Shimizu, T. S. & Berg, H. C. (2007). In vivo measurement by FRET of pathway activity in bacterial chemotaxis. Methods Enzymol 423:365-391.

Shimizu, T. S., Delalez, N., Pichler, K. & Berg, H. C. (2006). Monitoring bacterial chemotaxis by using bioluminescence resonance energy transfer: absence of feedback from the flagellar motors. PNAS 103:2093-2097.

Korobkova, E., Emonet, T., Vilar, J. M., Shimizu, T. S. & Cluzel, P. (2004). From molecular noise to behavioural variability in a single bacterium. Nature 428:574-578.

Shimizu, T. S., Aksenov, S. V. & Bray, D. (2003). A spatially extended stochastic model of the bacterial chemotaxis signalling pathway. J Mol Biol 329:291-309.

Levin, M D, Shimizu, T. S. & Bray, D. (2002). Binding and diffusion of CheR molecules within a cluster of membrane receptors. Biophys J 82:1809-1817.

Le Novère, N. & Shimizu, T. S.. (2001). StochSim: modelling of stochastic biomolecular processes. Bioinformatics 17:575-576.

Shimizu, T. S., Le Novère, N., Levin, M. D., Beavil, A. J., Sutton, B. J. & Bray, D. (2000). Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis. Nature Cell Biol 2:792-796.

Morton-Firth, C. J., Shimizu T. S. & Bray D. (1999).  A Free-energy-based Stochastic Simulation of the Tar Receptor Complex.  J Mol Biol 286:1059-1074.