2013

• Gian Marco Palamara, Gustav W. Delius, Matthew J. Smith, and Owen L. Petchey, Predation effects on mean time to extinction under demographic stochasticity, in Journal of Theoretical Biology, Elsevier, June 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
• 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

• 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
• 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
• 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
• 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
• Neil Dalchau, Understanding biological timing using mechanistic and black-box models, in New Phytologist, vol. 193, no. 4, pp. 852-858, March 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

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
• 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
• 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
• 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
• Neil Dalchau and Alex AR Webb, Ticking over - Circadian systems across the kingdoms of life, in Biochemist, vol. 33, no. 1, 1 February 2011

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
• 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
• 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
• 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

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
• 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
• 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
• 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
• 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

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
• 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
• 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
• 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

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

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
• 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

2013

• 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

2011

• 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

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

2008

• Andrew Phillips, Specifying and Implementing Secure Mobile Applications, in Process Algebra for Parallel and Distributed Processing , Chapman & Hall/CRC, December 2008

2006

• Editors, Stephen Emmott, Ehud Shapiro, Stuart Rison, Andrew Phillips, and Andrew Herbert, Towards 2020 Science, Microsoft, March 2006

2013

• Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, and Hillel Kugler, Z34Bio: An SMT-based Framework for Analyzing Biological Computation, in SMT'13, July 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

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

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
• D. Harel and H. Kugler, Some Thoughts on the Semantics of Biocharts, in Essays in Memory of Amir Pnueli, Springer Verlag, 2010

2009

• H. Kugler and I. Segall, Compositional Synthesis of Reactive Systems from Live Sequence Chart Specifications, in Tools and Algorithms for the Construction and Analysis of Systems (TACAS'09), Springer Verlag, March 2009
• H. Kugler, C. Plock, and A. Pnueli, Controller Synthesis from LSC Requirements, in Fundamental Approaches to Software Engineering (FASE'09), Springer Verlag, March 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

• 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
• 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
• 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

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
• 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