Tom Shimizu

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Member of: Systems Biology

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Tom Shimizu received his Ph.D. from the University of Cambridge in 2003, working on biophysical problems of intracellular signaling using stochastic methods. In 2003-2009 he held a postdoctoral fellowship at Harvard University, where he developed Förster resonance energy transfer (FRET) experiments in live bacteria. In 2009, he joined the faculty of FOM Institute AMOLF as a Group Leader. His research group develops biophysical experiments and theoretical models to bridge dynamics at the scale of molecules, cells and whole organisms.

Curriculum Vitae

Selected publications:

Taute, K.M., Gude, S., Tans, S.J. & Shimizu, T.S. (2015). High-throughput 3D tracking of bacteria on a standard phase contrast microscope. Nature Commun 6:8776.

Helms, S.J., Avery, L., Stephens, G.J. & Shimizu, T.S. (2015). Modeling the ballistic-to-diffusive transition in nematode motility reveals low-dimensional behavioral variation across species. arXiv:1501.00481.

Flores, M., Shimizu, T. S., ten Wolde, P. R. & Tostevin, F. (2012). Signalling noise enhances chemotactic drift of E. coli. Phys Rev Lett 109:148101.

Lazova, M. D., Butler, M. T., Shimizu, T. S. & Harshey, R.M. (2012). Salmonella chemoreceptors McpB and McpC mediate a repellent response to L-cystine: a potential mechanism to avoid oxidative conditions. Mol Microbiol 84:697–711.

Lazova, M. D., Ahmed, T., Bellomo, D., Stocker, R. & Shimizu, T. S. (2011). Response rescaling in bacterial chemotaxis. PNAS 108:33870-33875.

Celani, A., Shimizu, T. S. & Vergassola, M. (2011). Molecular and functional aspects of bacterial chemotaxis. J Stat Phys 144:219-240.

Ahmed, T., Shimizu, T. S. & Stocker, R. (2010). Microfluidics for bacterial chemotaxis. Integrative Biology 2:604-629.

Ahmed, T., Shimizu, T. S. & Stocker, R. (2010). Bacterial chemotaxis in linear and nonlinear steady microfluidic gradients. Nano Letters 10:3379-3385.

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.

Publications

  • Kristin Aleklett, E.Toby Kiers, Pelle Ohlsson, Thomas S. Shimizu, Victor E.A. Caldas and Edith C. Hammer, Build your own soil : exploring microfluidics to create microbial habitat structures, ISME J. ASAP article, (2017)

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  • Eric Johlin, Jacopo Solari, Sander A. Mann, Jia Wang, Tom S. Shimizu and Erik C. Garnett, Super-Resolution Imaging of Light-Matter Interactions near Single Semiconductor Nanowires, Nature Commun. 7, 13950: 1-6 (2016)

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  • K.M. Taute, S. Gude, S.J. Tans and T.S. Shimizu, High-throughput 3D tracking of bacteria on a standard phase contrast microscope, Nature Commun. 6, 8776: 1-9 (2015)

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  • Marlo Flores, Thomas S. Shimizu, Pieter Rein ten Wolde and Filipe Tostevin, Signaling noise enhances chemotactic drift of E. coli, Phys. Rev. Lett. 109, 14: 148101 1-5 (2012)

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  • Milena D. Lazova, Mitchell T. Butler, Thomas S. Shimizu and Rasika M. Harshey, Salmonella chemoreceptors McpB and McpC mediate a repellent response to L-cystine: a potential mechanism to avoid oxidative conditions, Mol. Microbiol. 84, 4: 697–711 (2012)

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  • Milena D. Lazova, Tanvir Ahmed, Domenico Bellomo, Roman Stocker and Thomas S. Shimizu, Response rescaling in bacterial chemotaxis, PNAS 108, 33: 13870–13875 (2011)

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  • A. Celani, T.S. Shimizu and M. Vergassola, Molecular and functional aspects of bacterial chemotaxis, J. Stat. Phys. 144, 2 : Statistical Mechanics and Biology: 219-240 (2011)

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  • Tanvir Ahmed, Thomas S. Shimizu and Roman Stocker, Microfluidics for bacterial chemotaxis, Integr. Biol. 2, 11-12: 604-629 (2010)

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  • Tanvir Ahmed, Thomas S. Shimizu and Roman Stocker, Bacterial chemotaxis in linear and nonlinear steady microfluidic gradients, Nano Lett. 10, 9: 3379–3385 (2010)

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  • Thomas S. Shimizu, Yuhai Tu and Howard C. Berg, A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli, Mol. Syst. Biol. 6, 382 1-14 (2010)

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