Bray, D. (2013) The propagation of allosteric states in large multiprotein complexes Journal of Molecular Biology In press.

Bray, D. (2012) What we do not know about cells (unpublished manuscript).

Bray, D. (2012) BRAIN versus MACHINE in Singularity Hypotheses: A Scientific and Philosophical Assessment (The Frontiers Collection) Eden, A. H., Moor, J. H., Søraker, J. H., & Steinhart, E., eds.) Springer-Verlag, London.

Bray, D. (2012) The cell as a thermostat: how much does it know? in Advances in Systems Biology (Goryanin, I. I., & Goryachev, A. B., eds.) Springer-Verlag, London. Advances in Experimental Medicine and Biology 736:193-198.

Goldman, J., Levin, M. D., & Bray, D. (2009) Signal amplification in a lattice of coupled protein kinases Molecular BioSystems 5:1853-1859.

DePristo, M. A., Chang, L., Vale R. D., Khan, S. M., & Lipkow, K. (2009) Introducing simulated cellular architecture to the quantitative analysis of fluorescent microscopy Progress in Biophysics and Molecular Biology 100:25-32.

Bray, D. (2009) Wetware Yale University Press, New Haven, CT (review by Marshall, W. F. Science 325:948).

Zonia, L., & Bray, D. (2009) Swimming patterns and dynamics of simulated Escherichia coli bacteria Journal of the Royal Society Interface 6:1035-1046.

Lipkow, K., & Odde, D. J. (2008) Model for protein concentration gradients in the cytoplasm Cellular and Molecular Bioengineering 1:84-92.

Bray, D., & Williams, D. (2008) How the "melting" and "freezing" of protein molecules may be used in cell signaling ACS Chemical Biology 3:89-91.

Silversmith, R. E., Levin, M. D., Schilling, E., & Bourret, R. B. (2008) Kinetic characterization of catalysis by the chemotaxis phosphatase CheZ: Modulation of activity by the CheYp substrate Journal of Biological Chemistry 283: 756-765.

Windisch, B., Bray, D., & Duke, T. (2007) Balls and chains-a mesoscopic approach to tethered protein domains Biophysical Journal 91:2383-2392.

Bray, D., Levin, M. D., & Lipkow, K. (2007) The chemotactic behavior of computer-based surrogate bacteria Current Biology 17:12-19.

Grati, M., Schneider, M. E., Lipkow, K., Strehler, E. E., Wenthold, R. J., & Kachar, B. (2006) Rapid turnover of stereocilia membrane proteins: evidence from the trafficking and mobility of plasma membrane Ca²⁺-ATPase 2 Journal of Neuroscience 26:6386-6395. (1.4 MB)

Fleire, S. J., Goldman, J. P., Carrasco, Y. R., Weber, M., Bray, D., & Batista, F. D. (2006) B cell ligand discrimination through a spreading and contraction response Science 312:738-741. (commentary by Harnett, M. M. ibid. 709-710).

Lipkow, K. (2006) Changing cellular location of CheZ predicted by molecular simulations PLoS Computational Biology 4:e39. (print-quality pdf (2.7 MB)).

Andrews, S. S. (2005) Serial rebinding of ligands to clustered receptors as exemplified by bacterial chemotaxis Physical Biology 2:111-122.

Bray, D. (2005) Flexible peptides and cytoplasmic gels Genome Biology 6:106.

Lipkow, K., Andrews, S. S., & Bray, D. (2005) Simulated diffusion of phosphorylated CheY through the cytoplasm of Escherichia coli Journal of Bacteriology 187:45-53 (commentary by Hazelbauer, G. L. ibid. 23-25).

Andrews, S. S., & Bray, D. (2004) Stochastic simulation of chemical reactions with spatial resolution and single molecule detail Physical Biology 1:137-151.

Goldman, J., Andrews, S., & Bray, D. (2004) Size and composition of membrane protein clusters predicted by Monte Carlo analysis European Biophysics Journal 33:506-512.

Bray, D., & Duke, T. (2004) Conformational spread: the propagation of allosteric states in large multiprotein complexes Annual Review of Biophysics and Biomolecular Structure 33:53-73.

Bray, D. (2003) Molecular networks: the top-down view Science 301:1864-1865.

Levin, M. D. (2003) Noise in gene expression as the source of non-genetic individuality in the chemotactic response of Escherichia coli FEBS Letters 550:135-138.

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

Bray, D. (2003) Molecular prodigality Science 299:1189-1190.

Shimizu, T. S., & Bray, D. (2002) Modelling the bacterial chemotaxis receptor complex Novartis Foundation Symposium 247:162-77; discussion 177-81. (7.9 MB)

Shimizu, T. S. (2002) The spatial organisation of cell signalling pathways - a computer-based study Ph. D. Thesis, University of Cambridge. (18.1 MB)

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

Bray, D. (2002) Bacterial chemotaxis and the question of gain Proceedings of the National Academy of Sciences USA 99:7-9.

Shimizu, T. S., & Bray, D. (2001) Computational cell biology - the stochastic approach in Foundations of Systems Biology (Kitano, H., ed.) The MIT Press, Cambridge, MA.

Bray, D. (2001) Reasoning for results Nature 412:863.

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

Duke, T. A. J., Le Novère, N., & Bray, D. (2001) Conformational spread in a ring of proteins: a stochastic view of allostery Journal of Molecular Biology 308:541-553. (2 MB)

Firth, C. A. J. M., & Bray, D. (2001) Stochastic simulation of cell signaling pathways in Computational Modeling of Genetic and Biochemical Networks (Bower, J. M., & Bolouri, H., eds.) The MIT Press, Cambridge, MA.

Bray, D. (2000) Cell Movements 2nd edition, Garland Publishing, New York, NY.

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 Biology 2:792-796 (commentary by Manson, M. D., & Cantwell, B. J. ibid. E199-E201).

Bray, D. (2000) Chaotic actin Genome Biology 1:reviews108.

Duke, T. A. J., & Bray, D. (1999) Heightened sensitivity of a lattice of membrane receptors Proceedings of the National Academy of Sciences USA 96:10104-10108.

Morton-Firth, C. J., Shimizu, T. S., & Bray, D. (1999) A free-enegy-based stochastic simulation of the Tar receptor complex Journal of Molecular Biology 286:1059-1074.

Morton-Firth, C. J. (1998) Stochastic simulation of cell signalling pathways Ph. D. Thesis, University of Cambridge. (9.6 MB)

Abouhamad, W. N., Bray, D., Schuster, M., Boesch, K. C., Silversmith, R. E., & Bourret, R. B. (1998) Computer-aided resolution of an experimental paradox in bacterial chemotaxis Journal of Bacteriology 180:3757-3764.

Bray, D. (1998) Signaling complexes: biophysical constraints on intracellular communication Annual Review of Biophysics and Biomolecular Structure 27:59-75.

Morton-Firth, C. J., & Bray, D. (1998) Predicting temporal fluctuations in an intracellular signalling pathway Journal of Theoretical Biology 192:117-128.

Bray, D., Levin, M. D., & Morton-Firth, C. J. (1998) Receptor clustering as a mechanism to control sensitivity Nature 393:85-88 (commentary by Barkai, N., & Leibler, S. ibid. 18-21).

Levin, M. D., Morton-Firth, C. J., Abouhamad, W. N., Bourret, R. B., & Bray, D. (1998) Origins of individual swimming behavior in bacteria Biophysical Journal 74:175-181.

Bray, D., & Lay, S. (1997) Computer-based analysis of the binding steps in protein complex formation Proceedings of the National Academy of Sciences USA 94:13493-13498 (commentary by Ferrell, J. E., Science's STKE, 3rd October, 2000).

Bray, D. (1997) Reductionism for biochemists: how to survive the protein jungle Trends in Biochemical Sciences 22:325-326.

Lay, S., & Bray, D. (1997) A computer program for the analysis of protein complex formation Computer Applications in the Biosciences 13:439-444.

Bray, D., & Bourret, R. B. (1995) Computer analysis of the binding reactions leading to a transmembrane receptor-linked multiprotein complex involved in bacterial chemotaxis Molecular Biology of the Cell 6:1367-1380. (2.3 MB)

Bray, D. (1995) Protein molecules as computational elements in living cells Nature 376:307-312. (8.4 MB)

Bray, D., & Lay, S. (1994) Rapid numerical integration algorithm for finding the equilibrium state of a system of coupled binding reactions Computer Applications in the Biosciences 10:471-476. (5.4 MB)

Bray, D., & Lay, S. (1994) Computer simulated evolution of a network of cell-signaling molecules Biophysical Journal 66:972-977. (1.3 MB)

Bray, D., Bourret, R. B., & Simon, M. I. (1993) Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis Molecular Biology of the Cell 4:469-482. (2.4 MB)

Bray, D. (1990) Intracellular signalling as a parallel distributed process Journal of Theoretical Biology 143:215-231. (1.1 MB)

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