Our group is conducting research to uncover fundamental principles of biological computation: what biological systems compute, and how this computation is performed. We are also developing methods for programming computation in biological systems. Our research currently focuses on fundamentals of Biological Computation, with applications in Immunology and Development, together with principles of Programming Life, with applications in DNA Computing and Synthetic Biology.
Current projects include designing molecular circuits made of DNA, and programming synthetic biological devices to perform complex functions over time and space. We also aim to understand the computation performed by cells during organ development, and how the adaptive immune system detects viruses and cancers, focusing on mechanism and function. We are tackling these questions through the development of computational models and domain-specific computational tools, in close collaboration with leading scientific research groups. The tools we develop are being integrated into a common software environment, which supports simulation and analysis across multiple scales and domains. This environment will serve as the foundation for a common language runtime for biological computation.
- DNA computing: Molecules reach consensus. Nature Nanotechnology, 4 October 2013.
- Computing with soup. The Economist, 3 March 2012.
- Computer-assisted genetic engineering. Technology Review, 3 August 2011.
- Coming Soon to a Lab Near You: Drag-and-Drop Virtual Worlds. Science, 11 February 2011.
- Tech Meets Bio. Nature Medicine, 26 August 2010.
Joint PhD scholars
- Alistair Bailey, Southampton University
- Frits Dannenberg, Oxford University
- Anton Kan, Cambridge University
- Wei Pan, Imperial College London
- Laura Parshotam, University College London
- Tim Rudge, Cambridge University
Former postdoctoral researchers
- Yuan-Jyue Chen, Neil Dalchau, Niranjan Srnivas, Andrew Phillips, Luca Cardelli, David Soloveichik, and Georg Seelig, Programmable chemical controllers made from DNA, in Nature Nanotechnology, Nature Publishing Group, 29 September 2013
- Antony N Dodd, Neil Dalchau, Michael J Gardner, Seong Jin Baek, and Alex AR Webb, The circadian clock has transient plasticity of period and is required for timing of nocturnal processes in Arabidopsis, in New Phytologist, 24 September 2013
- Matthew R. Lakin, Andrew Phillips, and Darko Stefanovic, Modular verification of DNA strand displacement networks via serializability analysis, in International Conference on DNA Computing and Molecular Programming, Springer Verlag, September 2013
- Boyan Yordanov, Christoph Wintersteiger, Youssef Hamadi, Andrew Phillips, and Hillel Kugler, Functional Analysis of Large-scale DNA Strand Displacement Circuits, in International Conference on DNA Computing and Molecular Programming, Springer, September 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, Neil Dalchau, Paul Grant, Jim Haseloff, Stephen Emmott, and Andrew Phillips, Automated Ratiometric Characterization using GEC, in International Workshop on Biodesign Automation, July 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
- 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
- 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
- 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
- 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
- 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
- Sara-Jane Dunn, Paul L. Appleton, Scott A. Nelson, Inke S. Nathke, David J. Gavaghan, and James M. Osborne, A Two-Dimensional Model of the Colonic Crypt Accounting for the Role of the Basement Membrane and Pericryptal Fibroblast Sheath, in PLoS Computational Biology, 24 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
- 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
- Neil Dalchau, Understanding biological timing using mechanistic and black-box models, in New Phytologist, vol. 193, no. 4, pp. 852-858, March 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
- 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
- Sara-Jane Dunn, Alexander G. Fletcher, S. Jonathan Chapman, David J. Gavaghan, and James M. Osborne, Modelling the role of the basement membrane beneath a growing epithelial monolayer, in Journal of Theoretical Biology, Elsevier, December 2011
- Matthew Lakin, Simon Youssef, Filippo Polo, Stephen Emmott, and Andrew Phillips, Visual DSD: a design and analysis tool for DNA strand displacement systems, in Bioinformatics, vol. 27, no. 22, pp. 3211–3213, Oxford University Press, November 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
- 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
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