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
- Kathryn Atwell, Oxford University
- Alistair Bailey, Southampton University
- Mattia Cinelli, University College London
- 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
- Boyan Yordanov, Jongmin Kim, Rasmus L. Petersen, Angelina Shudy, Vishwesh V. Kulkarni, and Andrew Phillips, Computational design of nucleic acid feedback control circuits, in ACS Synthetic Biology, American Chemical Society (In Press), July 2014
- Nicola Paoletti, Boyan Yordanov, Youssef Hamadi, Christoph M. Wintersteiger, and Hillel Kugler, Analyzing and Synthesizing Genomic Logic Functions, in CAV'14, Springer, July 2014
- Sara-Jane Dunn, Graziano Martello, Boyan Yordanov, Stephen Emmott, and Austin Smith, Defining an essential transcriptional factor program for naïve pluripotency, in Science, vol. 344, no. 6188, pp. 1156 - 1160, 6 June 2014
- Matthew R. Lakin, Rasmus Petersen, Kathryn E. Gray, and Andrew Phillips, Abstract modelling of tethered DNA circuits, in International Conference on DNA Computing and Molecular Programming, Springer, June 2014
- Neil Dalchau, Georg Seelig, and Andrew Phillips, Computational design of reaction-diffusion patterns using DNA-based chemical reaction networks, in International Conference on DNA Computing and Molecular Programming, Springer, June 2014
- Maria Bruna, Jonathan Chapman, and Matthew J Smith, Model reduction for slow-fast stochastic systems with metastable behaviour, in Journal of Chemical Physics, American Institute of Physics, April 2014
- Boyan Yordanov, Neil Dalchau, Paul Grant, Michael Pedersen, Stephen Emmott, Jim Haseloff, and Andrew Phillips, A Computational Method for Automated Characterization of Genetic Components, in ACS Synthetic Biology, American Chemical Society, 14 March 2014
- James Osborne, Miguel Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg McInerny, Gary Mirams, Joe Pitt-Francis, Biswa Sengupta, David Wright, Christian Yates, David Gavaghan, Stephen Emmott, and Charlotte Deane, Ten simple rules for effective computational research, in PLoS Computational Biology, vol. 10, no. 3, pp. e1003506, PLoS Computational Biology (Public Library of Science Computational Biology), , March 2014
- Michael Pedersen, Nicolas Oury, Colin Gravill, and Andrew Phillips, Bio Simulators: a web UI for biological simulation., in Bioinformatics, Oxford University Press, February 2014
- Matthew R. Lakin and Andrew Phillips, Compiling DNA Strand Displacement Reactions Using a Functional Programming Language, in Practical Aspects of Declarative Languages - 16th International Symposium, Springer, January 2014
- 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, vol. 8, no. 10, pp. 755-762, 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, vol. 201, no. 1, pp. 168-179, 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, vol. 8141, pp. 133-146, 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, vol. 8141, pp. 189-203, 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
- 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), , 14 March 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
- 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
- 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
- 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
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