prof.dr. Tom Shimizu

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Group leader: Physics of Behavior

CV / Biography

Tom Shimizu received his Ph.D. from the University of Cambridge in 2003, working on biophysical problems of intracellular signaling using stochastic methods. He subsequently 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 AMOLF as a Group Leader, and since 2015 also holds a joint appointment as Professor in the Department of Physics and Astronomy, Vrij Universiteit Amsterdam. His research group develops biophysical experiments, theoretical models, and data analysis methods to bridge dynamics at the scale of molecules, cells and whole organisms.

Curriculum Vitae

Selected publications:

Werner, S., Rozemuller, W.M., Ebbing, A., Alemany, A., Traets, J.J.H, van Zon, J.S., van Oudenaarden, A., Korswagen, H.C., Stephens, G.J. & Shimizu, T.S. (2020). Functional modules from variable genes: Leveraging percolation to analyze noisy, high-dimensional data. bioRxiv.

Gude, S., Pinçe, E., Taute, K.M., Seinen, A.B., Shimizu, T.S.* and Tans, S.J.* (2020). Bacterial coexistence driven by motility and spatial competition. Nature 578, 588-592.

Wu, F., Swain, P., Kuijpers, L., Zheng, X., Felter, K., Guurink, M., Solari, J., Jun, S., Shimizu, T.S., Chaudhuri, D. Mulder, B. & Dekker, C. (2019). Cell boundary confinement sets the size and position of the E. coli chromosome. Curr Biol 29, 2131-2144.

Whiteside, M.D., Werner, G.D., Caldas, V.E., van’t Padje, A., Dupin, S.E., Elbers, B., Bakker, M., Wyatt, G.A., Klein, M., Hink, M.A. and Postma, M., Vailtla, B., Noe, R., Shimizu, T.S., West, S.A. & Kiers, E.T. (2019). Mycorrhizal fungi respond to resource inequality by moving phosphorus from rich to poor patches across networks. Curr Biol 29, 2043-2050.

Helms, S.J., Rozemuller, M.W., Costa, A.C., Avery, L., Stephens, G.J. & Shimizu, T.S. (2019). Modelling the ballistic-to-diffusive transition in nematode motility reveals variation in exploratory behaviour across species. J R Soc Interface 16, 157.

Koler, M., Peretz, E., Aditya, C., Shimizu, T.S. & Vaknin, A. (2018). Long-term positioning and polar preference of chemoreceptor clusters in E. coli, Nature Commun 9, 4444.

Solari, J., Anquez, F., Scherer, K. & Shimizu, T.S. (2018). Bacterial chemoreceptor imaging at high spatio-temporal resolution using photoconvertible fluorescent proteins. Meth Mol Biol 1729, 203-231.

Keegstra, J.M., Kamino, K., Anquez, F., Lazova, M.D., Emonet, T. & Shimizu, T.S.  (2017). “Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET.” eLife 6, e27455.

Johlin, E., Solari, J., Mann, S.A., Wang, J., Shimizu, T.S. & Garnett, E.C. (2016). Super-Resolution Imaging of Light-Matter Interactions near Single Semiconductor Nanowires, Nature Commun 7, 13950.

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.

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

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., 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.

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.