Publications per research area

2009

• Matthew J. Smith, Jens D. M. Rademacher, and Jonathan A. Sherratt, Absolute stability of wavetrains can explain spatiotemporal dynamics in reaction-diffusion systems of lambda-omega type, in SIAM Journal of Applied Dynamical Systems, 8(3), 1136-1159, 27 August 2009
• Jonathan A. Sherratt, Matthew J. Smith, and Jens D.M. Rademacher, Locating the transition from periodic oscillations to spatiotemporal chaos in the wake of invasion, in Proceedings of that National Academy of Sciences of the United States of America, 106(27), pp. 10890-10895, 7 July 2009
• Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanogullari, and Andrew Phillips, A Process Model of Rho GTP-binding Proteins, in Theoretical Computer Science, Elsevier , 18 May 2009
• Matthew J. Smith, Sandra Telfer, Eva R. Kallio, Sarah Burthe, Alex R. Cook, Xavier Lambin, and Michael Begon, Host-pathogen time series data in wildlife support a transmission function between density and frequency dependence, in Proceedings of the National Academy of Sciences of the United States of America, 106(19), pp. 7905-7909, 12 May 2009
• Michael Pedersen and Andrew Phillips, Towards programming languages for genetic engineering of living cells, in Journal of the Royal Society Interface, 15 April 2009
• Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanogullari, and Andrew Phillips, A Process Model of Actin Polymerisation, in Electronic Notes in Theoretical Computer Science, vol. 229, no. 1, pp. 127-144, Elsevier , February 2009
• Begon, M., Telfer, S., Smith, M.J., Burthe, S., Paterson, S., Lambin, and X., Seasonal host dynamics drive the timing of recurrent epidemics in a wildlife, in Proceedings of the Royal Society B: Biological Sciences, 20 January 2009
• Eric L. Berlow, Jennifer A. Dunne, Neo D. Martinez, Phillip B. Stark, Richard J. Williams, and Ulrich Brose, Simple prediction of interaction strengths in complex food webs, in Proceedings of the National Academy of Sciences of the USA, vol. 106, pp. 187-191, Proceedings of the National Academy of Sciences, 6 January 2009
• T. Guilford, J. Meade, J. Willis, R.A. Phillips, D. Boyle, S. Roberts, M. Collett, R. Freeman, and C.M. Perrins, Migration and stopover in a small pelagic seabird, the Manx Shearwater Puffinus puffinus: insights from machine learning, in Proc. Roy. Soc. London Ser. B, 2009
• McInerny, G J., Turner, J R G., Wong, H Y., Travis, J M J., Benton, and T G., How range shifts induced by climate change affect neutral evolution, in Proceedings of the Royal Socitey B., 2009
• D. Harel, H. Kugler, S. Maoz, and I. Segall, How Hard is Smart Play-Out? On the Complexity of Verification-Driven Execution, in Perspectives in Concurrency Theory (Festschrift for P.S. Thiagarajan), (K. Lodaya et al, eds.), University Press (India), 2009

2008

• Setty Y., Cohen I.R., Dor Y., and Harel D., Four-dimensional realistic modeling of pancreatic organogenesis, in Proc Natl Acad Sci U S A, December 2008
• Matthew J. Smith, The application of population modelling techniques to the development of Non-detriment Findings for Galanthus elwesii in Turkey., in International Expert Workshop on CITES Non-Detriment Findings, 17 November 2008
• Nikolay Strigul, Denis Pristinski, Drew W Purves, Jonathan Dushoff, and Stephen W Pacala, Scaling from trees to forests: tractable macroscopic equations for forest dynamics, in Ecological Monographs, vol. 78, no. 4, pp. 523-545, November 2008
• Harel, D., Segall, I., Kugler, H., Setty, and Y., Crafting Game-Models using Reactive System Design , in Future Play, Association for Computing Machinery, Inc., November 2008
• Drew W Purves, Jeremy W Lichstein, Nikolay Strigul, and Stephen W Pacala, Predicting and understanding forest dynamics using a simple tractable model, in Proceedings of the National Academy of Sciences USA, 29 October 2008
• M. Begon, S. Telfer, S. Burthe, X. Lambin, M. Smith, and S. Paterson, Effects of abundance on infection in natural populations: field voles and cowpox virus., in Epidemics, 6 October 2008
• Lindsay A Turnbull, Mark Rees, and Drew W Purves, Why equalising trade-offs aren’t always neutral, in Ecology Letters, vol. 11, pp. 1037-1046, October 2008
• Matthew Smith, Jonathan Sherratt, and Xavier Lambin, The effects of density dependent dispersal on the spatiotemporal dynamics of cyclic populations, in Journal of Theoretical Biology, Elsevier Ltd., 21 September 2008
• Kam N., Kugler H., Marelly R., Appleby L., Fisher J., A. Pnueli, D. Harel, M.J. Stern, and E.J.A. Hubbard, A scenario-based approach to modeling development: A prototype model of C. elegans vulval fate specification , in Developmental Biology, Elsevier , August 2008
• P. Combes, D. Harel, and H. Kugler, Modeling and Verification of a Telecommunication Application using Live Sequence Charts and the Play-Engine Tool, in Software and Systems Modeling, vol. 7, no. 2, March 2008
• Ralf Blossey, Luca Cardelli, and Andrew Phillips, Compositionality, Stochasticity and Cooperativity in Dynamic Models of Gene Regulation, in HFSP Journal, vol. 2, no. 1, pp. 17–28, HFSP Publishing, February 2008
• T Guilford, J Meade, R Freeman, T Evans, F Bonadonna, D Boyle, and C M Perrins, GPS tracking of the foraging movements of Manx Shearwaters Puffinus puffinus breeding on Skomer Island, Wales., in Ibis, January 2008
• J. Fisher, T.A. Henzinger, M. Mateescu, and N. Piterman, Bounded Asynchrony: A biologically-inspired notion of concurrency, in Proceedings of FMSB ’08 Cambridge, UK, Springer, January 2008
• Richard J. Williams and Neo D. Martinez, Success and its limits among structural models of complex food webs, in Journal of Animal Ecology, January 2008
• Lindsay A Turnbull, Cloe Paul-Victor, Bernhard Schmid, and Drew W Purves, Growth rates, seed size and physiology - Do small-seeded species really grow faster?, in Ecology, vol. 89, pp. 1352-1363, January 2008
• Sadot A., Fisher J., Barak D., Admanit Y., Stern M.J., Hubbard E.J.A., and Harel D., Towards Verified Biological Models, in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, pp. 1-12, January 2008
• Fergus P. Massey, Matthew J. Smith, Xavier Lambin, and Sue E. Hartley, Are silica defences in grasses driving vole population cycles?, in Biology Letters, January 2008
• J. A. Dunne, R.J. Williams, N.D. Martinez, R.A. Wood, and D.H. Erwin, Compilation and network analyses of Cambrian food webs, in PLoS Biology, vol. 6, January 2008
• Richard J. Williams, Effects of network and dynamical model structure on species persistence in large model food webs, in Theoretical Ecology, January 2008
• William J. Sutherland, Mark J. Bailey, Ian P. Bainbridge, Tom Brereton, Jaimie T. A. Dick, Joanna Drewitt, Nicholas K. Dulvy, Nicholas R. Dusic, Robert P. Freckleton, Kevin J. Gaston, Pam M. Gilder, Rhys E. Green, A. Louise Heathwaite, Sally M. Johnson, David W. Macdonald, Roger Mitchell, Daniel Osborn, Roger P. Owen, Jules Pretty, Stephanie V. Prior, Havard Prosser, Andrew S. Pullin, Paul Rose, Andrew Stott, Tom Tew, Chris D. Thomas, Des B. A. Thompson, Juliet A. Vickery, Matt Walker, Clive Walmsley, Stuart Warrington, Andrew R. Watkinson, Rich J. Williams, Rosie Woodroffe, and Harry J. Woodroof, Future novel threats and opportunities facing UK biodiversity identified by horizon scanning, in Journal of Applied Ecology, January 2008
• L. Church, K. Apagyi, and J. Fisher, Languages for Biological Models: Importance, Implications and Challenges - A Work In Progress, in Proceedings of the Psychology of Programming Interest Group, January 2008

2007

• H. Kugler, C. Plock, and A. Pnueli, Synthesizing Reactive Systems from LSC Requirements using the Play-Engine, in Companion to the 22nd ACM SIGPLAN conference on object oriented programming systems and applications (OOPSLA’07), October 2007
• Thomas P Adams, Drew W Purves, and Stephen W Pacala, Understanding height-structured competition in forests: is there an R* for light?, in Proceedings of the Royal Society Series B, vol. 274, no. 1628, pp. 3039-3047, January 2007
• Drew W Purves, Jeremy W Lichstein, and Stephen W Pacala, Crown Plasticity and Competition for Canopy Space: A New Spatially Implicit Model Parameterized for 250 North American Tree Species, in PLoS-One, vol. 2, no. 9, pp. e870, January 2007
• Marc Schaub, April Bezdek, Thomas Henzinger, Freddy Radtke, and Jasmin Fisher, Qualitative Crosstalk Analysis of Wnt and Notch Signaling in Mammalian Skin, in RECOMB Systems Biology, ’07 San Diego, CA, Springer, January 2007

2006

• U. Brose, T. Jonsson, E. L. Berlow, P. Warren, C. Banasek-Richter, L. F. Bersier, J. L. Blanchard, T. Brey, S. R. Carpenter, M. F. C. Blandenier, L. Cushing, H. A. Dawah, T. Dell, F. Edwards, S. Harper-Smith, U. Jacob, M. E. Ledger, N. D. Martinez, J. Memmott, K. Mintenbeck, J. K. Pinnegar, B. C. Rall, T. S. Rayner, D. C. Reuman, L. Ruess, W. Ulrich, R. J. Williams, G. Woodward, and J. E. Cohen, Consumer-resource body-size relationships in natural food webs, in Ecology, vol. 87, no. 10, pp. 2411-2417, January 2006

2010

• Fisher J. and Harel D., On Statecharts for Biology, in Symbolic Systems Biology: Theory and Methods, Jones and Bartlett Publishers, 2010

2009

• Andrew Phillips, A Visual Process Calculus for Biology, in Symbolic Systems Biology: Theory and Methods, Jones and Bartlett Publishers, In Press, 2009

2007

• T Guilford, J Meade, R Freeman, C M Perrins, D Biro, T Evans, F Bonadonna, and D Boyle, Tracking the foraging movements of Manx Shearwaters from Skomer Island by GPS, January 2007

2008

• Matthew J. Smith, The application of population modelling techniques to the development of Non-detriment Findings for Galanthus elwesii in Turkey., in International Expert Workshop on CITES Non-Detriment Findings, 17 November 2008