T
Thomas S. Shimizu
Researcher at University of Cambridge
Publications - 32
Citations - 6350
Thomas S. Shimizu is an academic researcher from University of Cambridge. The author has contributed to research in topics: Chemotaxis & Kinase activity. The author has an hindex of 18, co-authored 27 publications receiving 5992 citations. Previous affiliations of Thomas S. Shimizu include Harvard University & Keio University.
Papers
More filters
Journal ArticleDOI
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Michael Hucka,Andrew Finney,Herbert M. Sauro,Hamid Bolouri,Hamid Bolouri,John Doyle,Hiroaki Kitano,Adam P. Arkin,Benjamin Bornstein,Dennis Bray,Athel Cornish-Bowden,Autumn A. Cuellar,S. Dronov,E. D. Gilles,Martin Ginkel,V. Gor,Igor Goryanin,W. J. Hedley,T. C. Hodgman,J.-H.S. Hofmeyr,Peter Hunter,Nick Juty,J. L. Kasberger,Andreas Kremling,Ursula Kummer,N Le Novère,Leslie M. Loew,D. Lucio,Pedro Mendes,E. Minch,Eric Mjolsness,Yoichi Nakayama,Melanie R. Nelson,Poul M. F. Nielsen,T. Sakurada,James C. Schaff,Bruce E. Shapiro,Thomas S. Shimizu,H. D. Spence,Jörg Stelling,Koichi Takahashi,Masaru Tomita,John Wagner,J. Wang +43 more
TL;DR: This work summarizes the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks, a software-independent language for describing models common to research in many areas of computational biology.
Journal ArticleDOI
E-CELL: software environment for whole-cell simulation.
Masaru Tomita,Kenta Hashimoto,Koichi Takahashi,Thomas S. Shimizu,Yuri Matsuzaki,Fumihiko Miyoshi,Kanako Saito,Sakura Tanida,Katsuyuki Yugi,J. C. Venter,Clyde A. Hutchison +10 more
TL;DR: E-CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed and a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis is constructed.
Journal ArticleDOI
From molecular noise to behavioural variability in a single bacterium
Ekaterina Korobkova,Thierry Emonet,Jose M. G. Vilar,Jose M. G. Vilar,Thomas S. Shimizu,Thomas S. Shimizu,Philippe Cluzel +6 more
TL;DR: It is shown that certain properties established by population measurements, such as adapted states, are not conserved at the single-cell level: for timescales ranging from seconds to several minutes, the behaviour of non-stimulated cells exhibit temporal variations much larger than the expected statistical fluctuations.
Journal ArticleDOI
Modeling the chemotactic response of Escherichia coli to time-varying stimuli
TL;DR: A general theoretical model based on receptor adaptation and receptor–receptor cooperativity is developed that provides a quantitative system-level description of the chemotaxis signaling pathway and can be used to predict E. coliChemotaxis responses to arbitrary temporal signals.
Journal ArticleDOI
A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli.
TL;DR: The results show how dynamic input–output measurements, time honored in physiology, can serve as powerful tools in deciphering cell‐signaling mechanisms.