2013

• Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, and Hillel Kugler, SMT-based Analysis of Biological Computation, in NASA Formal Methods Symposium 2013, Springer Verlag, May 2013
• Cory Merow, John A. Silander, and Matthew J. Smith, A practical guide to MaxEnt for modeling species' distributions: what it does, and why inputs and settings matter, in Ecography, Wiley, April 2013
• K. M. Young, K. Psachoulia, R. B. Tripathi, S-J. Dunn, L. Cossell, D. Attwell, K. Tohyama, and W. D. Richardson, Oligodendrocyte dynamics in the healthy adult CNS: evidence for myelin remodelling, in Neuron, 6 March 2013
• Maurizio Sajeva, Claudio Augugliaro, Matthew Smith, and Elisabetta Oddo, Regulating Internet Trade in CITES Species, in Conservation Biology, Wiley, 8 February 2013
• Mindy M. Syfert, Matthew J. Smith, and David A. Coomes, The effects of sampling bias and model complexity on the predictive performance of MaxEnt species distribution models , in PLOS One, vol. 8, no. 2, PLoS, February 2013
• M. J. Smith, D. W. Purves, M. C. Vanderwel, V. Lyutsarev, and S. Emmott, The climate dependence of the terrestrial carbon cycle, including parameter and structural uncertainties, in Biogeosciences, vol. 10, pp. 583-606, European Geosciences Union, 29 January 2013
• Drew W Purves, Jorn P W Scharlemann, Mike Harfoot, Tim Newbold, Derek Tittensor, Jon Hutton, and Stephen Emmott, Time to Model All Life on Earth, in Nature, vol. 493, no. 7432, pp. 295-297, Nature Publishing Group, 17 January 2013
• Raul Garcia-Valdes, Miguel A Zavala, Migueal B Araujo, and Drew W Purves, Chasing a moving target: projecting climate change-induced shifts in non-equilibrial tree species distributions, in Journal of Ecology, British Ecological Society, January 2013
• Mark C Vanderwel, David A Coomes, and Drew W Purves, Quantifying variation in forest disturbance, and its effects on aboveground biomass dynamics, across the eastern United States, in Global Change Biology, Wiley, January 2013
• Noel McGough, David Kikodze, Richard Wilford, Lucy Garrett, Grigol Deisadze, Natalie Jaworska, and Matthew J. Smith, Assessing non-detrimental trade for a CITES Appendix II-listed plant species: the status of wild and cultivated Galanthus woronowii in Georgia, in Oryx, The International Journal of Conservation, Cambridge Journals, 2013
• G. R. Mirams, C. J. Arthurs, M. O. Bernabeu, R. Bordas, J. Cooper, A. Corrias, Y. Davit, S-J. Dunn, A. G. Fletcher, D. G. Harvey, M. E. Marsh, J. M. Osborne, P. Pathmanathan, J. Pitt-Francis, J. Southern, N. Zemzemi, and D. J. Gavaghan, Chaste: An Open Source C++ Library for Computational Physiology and Biology, in PLOS Comput. Biol., PLoS Computational Biology (Public Library of Science Computational Biology), , 2013

2012

• Tim Newbold, Jorn P W Scharlemann, Stuart H M Butchart, Cagan A Sekercioglu, Rob Alkemade, Hollie Booth, and Drew W Purves, Ecological traits affect the response of tropical forest bird species to land-use intensity, in Proceedings of the Royal Society of London, Series B, The Royal Society, November 2012
• Matthew J. Smith, Mark C. Vanderwel, Vassily Lyutsarev, Stephen Emmott, and Drew W. Purves, The climate dependence of the terrestrial carbon cycle; including parameter and structural uncertainties, in Biogeosciences Discussions, vol. 9, pp. 13439-13496, European Geosciences Union, 4 October 2012
• Tim Newbold, Stuart Butchart, Cagan Sekercioglu, Drew Purves, and Jorn Scharlemann, Mapping Functional Traits: Comparing Abundance and Presence-Absence Estimates at Large Spatial Scales, in PLoS ONE, vol. 7, no. 8, PLoS, 31 August 2012
• Timothy J. Rudge, Paul J. Steiner, Andrew Phillips, and Jim Haseloff, Computational Modeling of Synthetic Microbial Biofilms, in ACS Synthetic Biology, vol. 1, no. 8, pp. 345-352, American Chemical Society, July 2012
• Matthew Lakin, David Parker, Luca Cardelli, Marta Kwiatkowska, and Andrew Phillips, Design and Analysis of DNA Strand Displacement Devices using Probabilistic Model Checking, in Journal of the Royal Society Interface, vol. 9, no. 72, pp. 1470-1485 , The Royal Society, July 2012
• Lindsay A Turnbull, Christopher D Philipson, Drew W Purves, and AndOthers, Plant growth rates and seed size: a re-evaluation, in Ecology, vol. 93, no. 6, pp. 1283-1289, Ecological Society of America, June 2012
• Matthew Lakin, Loïc Paulevé, and Andrew Phillips, Stochastic Simulation of Multiple Process Calculi for Biology, in Theoretical Computer Science, vol. 431, pp. 181-206, Elsevier, May 2012
• Neil Dalchau, Matthew Smith, Samuel Martin, James R Brown, Stephen Emmott, and Andrew Phillips, Towards the rational design of synthetic cells with prescribed population dynamics, in Journal of the Royal Society Interface, vol. 9, pp. 2883-2898, The Royal Society, May 2012
• Silvia Caldararu, Paul Palmer, and Drew Purves, Inferring Amazon leaf demography from satellite observations of leaf area index, in Biogeosciences, European Geosciences Union, April 2012
• Matthew Lakin, Simon Youssef, Luca Cardelli, and Andrew Phillips, Abstractions for DNA circuit design, in Journal of the Royal Society Interface, vol. 9, no. 68, pp. 470-486, The Royal Society, March 2012
• Emily R Lines, Miguel A Zavala, Drew W Purves, and David A Coomes, Predictable changes in aboveground allometry of trees along gradients of temperature, aridity and competition, in Global Ecology and Biogeography, Wiley, February 2012
• Yaki Setty, Diana Dalfó, Dorota Z. Korta, E. Jane Albert Hubbard, and Hillel Kugler, A model of stem cell population dynamics: in-silico analysis and in-vivo validation, in Development, vol. 139, pp. 47 - 56, January 2012
• Jonathan A. Sherratt and Matthew J. Smith, Transition to Spatiotemporal Chaos Via Stationary Branching Shocks and Holes, in Physica D: Nonlinear Phenomena, Elsevier, 2012
• Jennifer J.H. Reynolds, Xavier Lambin, Fergus P. Massey, Stefan Reidinger, Jonathan A. Sherratt, Matthew J. Smith, Andrew White, and Sue E. Hartley, Delayed induced silica defences in grasses and their potential for destabilising herbivore population dynamics, in Oecologia, Springer, 2012
• Greg J. McInerny and Rampal S. Etienne, Stitch the niche – a practical philosophy and visual schematic for the niche concept, in Journal of Biogeography, vol. 39, no. 12, pp. 2103–2111, 2012
• Greg J. McInerny and Rampal S. Etienne, Pitch the niche – taking responsibility for the concepts we use in ecology and species distribution modelling, in Journal of Biogeography, vol. 39, no. 12, pp. 2112–2118, 2012
• Glenn Marion, Greg J. McInerny, Jörn Pagel, Stephen Catterall, Alex R. Cook, Florian Hartig, and Robert B. O'Hara, Parameter and uncertainty estimation for process-oriented population and distribution models: data, statistics and the niche, in Journal of Biogeography, vol. 39, no. 12, pp. 2225–2239, 2012
• Greg J. McInerny and Rampal S. Etienne, Ditch the niche – is the niche a useful concept in ecology or species distribution modelling?, in Journal of Biogeography, vol. 39, no. 12, pp. 2096–2102, 2012

2011

• Caspersen, John P., Vanderwel, Mark C., Cole, William G., Purves, and Drew W., How stand productivity results from size- and competition-dependent growth and mortality, in PLoS ONE, vol. 6, no. 12, pp. e28660, December 2011
• Neil Dalchau, Andrew Phillips, Leonard D Goldstein, Mark Howarth, Luca Cardelli, Stephen Emmott, Tim Elliott, and Joern M Werner, A peptide filtering relation quantifies MHC class I peptide optimization, in PLoS Computational Biology, vol. 7, no. 10, pp. e1002144, PLoS, 13 October 2011
• Richard J. Williams and Drew W. Purves, The probabilistic niche model reveals substantial variation in the niche structure of empirical food webs, in Ecology, 19 September 2011
• Y. Setty, C.C. Chen, M. Secrier, N. Skoblov, D. Kalamatianos, and S. Emmott, How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex, in BMC Systems Biology, Biomed Central, September 2011
• Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, and John Reif, Localized Hybridization Circuits, in International Conference on DNA Computing and Molecular Programming, vol. 6937, pp. 64-83, Springer Verlag, September 2011
• Matthew Lakin and Andrew Phillips, Modelling, simulating and verifying Turing-powerful strand displacement systems, in International Conference on DNA Computing and Molecular Programming , vol. 6937, pp. 130-144, Springer Verlag, September 2011
• C.E. Timothy Paine, Toby R Marthews, Deborah R Vogt, Drew Purves, Mark Rees, Andy Hector, and Lindsay A Turnbull, How to fit nonlinear plant growth models and calculate growth rates: an update for ecologists, in Methods in Ecology and Evolution, British Ecological Society, September 2011
• Hillel Kugler, Cory Plock, and Andy Roberts, Synthesizing Biological Theories, in Computer Aided Verification (CAV'11), Springer Verlag, July 2011
• Aleks Milicevic and Hillel Kugler, Model Checking Using SMT and Theory of Lists , in Nasa Formal Methods Symposium , Springer Verlag, April 2011
• Neil Dalchau, Seong Jin Baek, Helen M Briggs, Fiona C Robertson, Antony N Dodd, Michael J Gardner, Matthew A Stancombe, Michael J Haydon, Guy-Bart Stan, Jorge M Goncalves, and Alex AR Webb, The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose, in PNAS, vol. 108, no. 12, pp. 5104-5109, Proceedings of the National Academy of Sciences, 22 March 2011
• Matthew J. Smith, Richard J. Williams, and Drew W. Purves, Boosting CITES Through Research, in Science, American Association for the Advancement of Science, 18 February 2011
• Neil Dalchau and Alex AR Webb, Ticking over - Circadian systems across the kingdoms of life, in Biochemist, vol. 33, no. 1, 1 February 2011
• Greg McInerny and Drew Purves, Fine-scale environmental variation in species distribution modelling: regression dilution, latent variables and neighbourly advice, in Methods in Ecology and Evolution, British Ecological Society, 25 January 2011
• Lucas N. Joppa and Richard J. Williams, The influence of single elements on nested community structure, in Methods in Ecology and Evolution, 2011
• Thierry, Aaron, Petchey, Owen L., Beckerman, Andrew P., Warren, Philip H., Williams, and Richard J., The consequences of size dependent foraging for food web topology, in Oikos, vol. 120, pp. 439-502, 2011
• Hoffman, D., Fay, D., Joppa, and L.N., Human Migration to Park Edges: Case Studies Critique Findings from Global-level Statistical Analysis, in Conservation and Society, vol. In Press, 2011
• Richard J. Williams, Biology, Methodology or Chance? The Degree Distributions of Bipartite Ecological Networks, in PLoS ONE, PLoS, 2011
• Higgins, S.N., Vander Zanden, M.J, Joppa, L.N., and Vadeboncoeur Y., Simultaneous top-down and bottom up control of phytoplankton biomass in lakes: the role of invasive dreissenid mussels and phosphorus, in Canadian Journal of Fisheries and Aquatic Sciences, vol. In Press, 2011
• Joppa, L.N., Roberts, D.L., Myers, N., Pimm, and S.L., Biodiversity hotspots house the majority of missing species., in Proceedings of the National Academy of Sciences, 2011
• Vanderwel, Mark C., Caspersen, John P., Malcolm, Jay R., Papaik, Michael J., Messier, and Christian, Structural changes and potential vertebrate responses following simulated partial harvesting of boreal mixedwood stands, in Forest Ecology and Management, vol. 261, pp. 1362-1371, 2011

2010

• Alexander A Barron, Drew W Purves, and Lars O Hedin, Facultative nitrogen fixation by canopy legumes in a lowland tropical forest , in Oecologia, Springer Verlag, November 2010
• Andrew Phillips, Matthew Lakin, and Loïc Paulevé, Stochastic Simulation of Process Calculi for Biology, in Electronic Proceedings in Theoretical Computer Science, vol. 40, pp. 1-5, November 2010
• Andy van Hateren, Ed James, Alistair Bailey, Andrew Phillips, Neil Dalchau, and Tim Elliott, The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding, in Tissue Antigens, vol. 76, no. 4, pp. 259 - 275, Wiley, October 2010
• Emily R Lines, David A Coomes, and Drew Purves, Influences of Forest Structure, Climate and Species Composition on Tree Mortality across the Eastern US, in PLoS-One, vol. 5, no. 10, PLoS, October 2010
• Robin Freeman, R Mann, T Guilford, and D Biro, Group decisions and individual differences: route fidelity predicts flight leadership in homing pigeons (Columba livia), in Biology Letters, The Royal Society, September 2010
• Loïc Paulevé, Simon Youssef, Matthew R. Lakin, and Andrew Phillips, A Generic Abstract Machine for Stochastic Process Calculi, in Computational Methods in Systems Biology, pp. 43--54, September 2010
• Drew Purves and Lindsay Turnbull, Different but equal: the implausible assumption at the heart of neutral theory, in Journal of Animal Ecology, vol. 79, no. 6, pp. 1215-1225, British Ecological Society, 3 August 2010
• Rich Williams, Ananthi Anandanadesan, and Drew Purves, The Probabilistic Niche Model Reveals the Niche Structure and Role of Body Size in a Complex Food Web, in PLoS-One, vol. 5, no. e12092, PLoS, August 2010
• Neil Dalchau, Katharine E Hubbard, Fiona C Robertson, Carlos T Hotta, Helen M Briggs, Guy-Bart Stan, Jorge M Goncalves, and Alex A R Webb, Correct biological timing in Arabidopsis requires multiple light signaling pathways, in PNAS, vol. 107, no. 29, pp. 13171-13176, Proceedings of the National Academy of Sciences, 1 July 2010
• H. Kugler, A. Larjo, and D. Harel, Biocharts: A Visual Formalism for Complex Biological Systems, in Journal of the Royal Society Interface, vol. 7, no. 48, pp. 1015-1024, July 2010
• R Mann, Robin Freeman, O Osborne, R Garnett, C Armstrong, J Meade, D Biro, T Guilford, and S Roberts, Objectively identifying landmark use and predicting flight trajectories of the homing pigeon using Gaussian processes, in The Royal Society Interface, The Royal Society, July 2010
• Heil, A., Smith, M.J., Brändle, and A., Future Development Environments for Computational Scientists, in EUD4Services: Workshop on End User Development of Software Services and Applications, Microsoft Research, 25 May 2010
• Joppa, L.N., Loarie, S.R., Nelson, and A., Measuring population growth around tropical protected areas: current issues and solutions, in Tropical Conservation Science, vol. 3, no. 2, pp. 117-121, 2010
• Joppa, L.N., Montoya, J., Sole, R., Sanderson, J., Pimm, and S.L., On nestedness in ecological networks, in Evolutionary and Ecology Research, vol. 12, no. 1, pp. 35-46, 2010
• D. Harel and H. Kugler, Some Thoughts on the Semantics of Biocharts, in Essays in Memory of Amir Pnueli, Springer Verlag, 2010
• Jonathan A. Sherratt, Matthew J. Smith, and Jens D. M. Rademacher, Patterns of sources and sinks in the complex ginzburg-landau equation with zero linear dispersion, in SIAM Journal of Applied Dynamical Systems, Society for Industrial and Applied Mathematics, 2010
• Matthew J. Smith, Hesiquio Benitez Diaz, Margarita A. Clemente-Munoz, John Donaldson, Jon Hutton, Noel H. McGough, David H. Morgan, Colman O'Criodian, Thomasina E. Oldfield, Uwe Schippmann, and Richard J. Williams, Assessing the impacts of international trade on CITES-listed species: current practices and opportunities for scientific research, in Biological Conservation, Elsevier, 2010
• Joppa, L.N., Pfaff, and A., Global Protected Area Impacts, in Proceedings Of The Royal Society B, pp. doi:10.1098/rspb.2010.1713, 2010
• D. Harel, H. Kugler, S. Maoz, and I. Segall, Accelerating Smart Play-Out, in SOFSEM 2010: Theory and Practice of Computer Science, Springer Verlag, January 2010
• Mathew G Lewsey, Alex M Murphy, Daniel MacLean, Neil Dalchau, Jack H Westwood, Keith Macaulay, Mark H Bennett, Michael Moulin, David E Hanke, Glen Powell, Alison G Smith, and John P Carr, Disruption of two defensive signaling pathways by a viral RNA silencing suppressor, in Molecular Plant-Microbe Interations, vol. 23, no. 7, pp. 835-845, 2010
• Forero-Medina, G., Joppa, and L.N., Colombia's protected area network: representativeness of global and national conservation priorities, in PLoS ONE, vol. 5, no. 10, 2010
• Joppa, L.N., Williams, C.K., Casper, G.S., Temple, and S.A., Environmental factors affecting sampling success of artificial cover objects, in Herpetological Conservation and Biology, vol. 5, no. 1, pp. 143-148, 2010
• Pimm, S.L., Jenkins, C., Joppa, L.N., Roberts, D., Russell, and G., How many endangered species remain to be discovered in Brazil?, in Natureza & Conservação, vol. 8, no. 1, pp. 71-77, 2010
• Daniel M. Tompkins, Alison M. Dunn, Matthew J. Smith, and Sandra Telfer, Wildlife Diseases – From Individuals To Ecosystems, in Journal of Animal Ecology, Wiley, 2010
• Joppa, L.N., Roberts, D.L., Pimm, and S.L., How Many Species of Flowering Plants Are There?, in Proceedings Of The Royal Society B, pp. doi: 10.1098/rspb.2010.1004, 2010

2009

• Dennis Wang, Luca Cardelli, Andrew Phillips, Nir Piterman, and Jasmin Fisher, Computational modeling of the EGFR network elucidates control mechanisms regulating signal dynamics, in BMC Systems Biology, vol. 3, no. 118, December 2009
• Richard Wilford and Matthew Smith, Drop by Drop, in Kew Magazine, December 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
• Katharine E Hubbard, Fiona C Robertson, Neil Dalchau, and Alex A R Webb, Systems analyses of circadian networks., in Molecular Biosystems, vol. 5, pp. 1502-1511, 3 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
• Andrew Phillips and Luca Cardelli, A programming language for composable DNA circuits, in Journal of the Royal Society Interface, 17 June 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
• Andrew Phillips, An Abstract Machine for the Stochastic Bioambient Calculus, in Electronic Notes in Theoretical Computer Science, vol. 227, pp. 143-159, Elsevier , January 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
• 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

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, Microsoft Research, 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, 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, vol. 323, no. 1, pp. 1-5, Elsevier , August 2008
• Drew W Purves and Stephen W Pacala, Predictive Models of Forest Dynamics, in Science, vol. 320, no. 5882, pp. 1452-1453, 13 June 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, pp. 157-175, Springer Verlag, 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
• 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
• 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
• 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
• Johannes Borgstroem, Andrew Gordon, and Andrew Phillips, A Chart Semantics for the Pi-calculus, in Electronic Notes in Theoretical Computer Science, vol. 194, no. 2, pp. 3–29, Elsevier, 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
• 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
• 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
• 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
• 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
• Daniel Montoya, Miguel A Zavala, Miguel A Rodriguez, and Drew W Purves, Animal Versus Wind Dispersal and the Robustness of Tree Species to Deforestation, in Science, vol. 320, no. 5882, pp. 1502-1504, 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

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
• Andrew Phillips and Luca Cardelli, Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus, in Computational Methods in Systems Biology, vol. 4695, pp. 184–199, Springer, September 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
• 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
• 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

• Andrew Phillips, Luca Cardelli, and Giuseppe Castagna, A Graphical Representation for Biological Processes in the Stochastic Pi-calculus, in Transactions in Computational Systems Biology, vol. 4230, pp. 123–152, Springer, November 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
• Ralf Blossey, Luca Cardelli, and Andrew Phillips, A Compositional Approach to the Stochastic Dynamics of Gene Networks, in Transactions in Computational Systems Biology, vol. 3939, no. 3939, pp. 99–122, Springer, January 2006

• Alberto Carignano, Ye Yuan, Neil Dalchau, Alex AR Webb, and Jorge M Goncalves, Understanding and predicting biological networks using linear system identification, in Systems and Synthetic Biology: A Systematic Approach (In press), Springer, 2013
• Drew Purves and Mark Vanderwel, (book chapter in press) Traits States and Rates: Understanding Coexistence in Forests , in Forests and Global Change, Cambridge University Press, 2012
• Jacob Beal, Andrew Phillips, Douglas Densmore, and Yizhi Cai, High-Level Programming Languages for Biomolecular Systems, in Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic Biology, Springer, 2011
• Fisher J. and Harel D., On Statecharts for Biology, in Symbolic Systems Biology: Theory and Methods, Jones and Bartlett Publishers, 2010
• Andrew Phillips, A Visual Process Calculus for Biology, in Symbolic Systems Biology: Theory and Methods, Jones and Bartlett Publishers, In Press, 2009
• Andrew Phillips, Specifying and Implementing Secure Mobile Applications, in Process Algebra for Parallel and Distributed Processing , Chapman & Hall/CRC, December 2008
• Editors, Stephen Emmott, Ehud Shapiro, Stuart Rison, Andrew Phillips, and Andrew Herbert, Towards 2020 Science, Microsoft, March 2006

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