Station B

Publications

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- A deep learning model for predicting next-generation sequencing depth from DNA sequence
  
  Jinny X. Zhang, Boyan Yordanov, Alexander Gaunt, Michael X. Wang, Peng Dai, Yuan-Jyue Chen, Kerou Zhang, John Z. Fang, Neil Dalchau, Jiaming Li, Andrew Phillips, David Yu Zhang
  
  Nature Communications | July 2021, Vol 12
  
  Publication Project
- A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction.
  
  Trevor Y. H. Ho, Alexander Shao, Zeyu Lu, Harri Savilahti, Filippo Menolascina, Lei Wang, Neil Dalchau, Baojun Wang
  
  Nature Communications | April 2021, Vol 12(1): pp. 2200-2200
  
  DOI Publication
- Interpretation of morphogen gradients by a synthetic bistable circuit
  
  Paul Grant, Gregory Szep, Om Patange, Jacob Halatek, Valerie Coppard, Attila Csikasz-Nagy, Jim Haseloff, James C. W. Locke, Neil Dalchau, Andrew Phillips
  
  Nature Communications | November 2020, Vol 11(5545)
  
  Publication Project
- Turing Patterning in Stratified Domains
  
  Andrew L. Krause, Vaclav Klika, Jacob Halatek, Paul Grant, Thomas L. Woolley, Neil Dalchau, Eamonn A. Gaffney
  
  Bulletin of Mathematical Biology | October 2020, Vol 82(136)
  
  Publication Publication Project
- Domain-specific programming languages for computational nucleic acid systems
  
  Matthew R. Lakin, Andrew Phillips
  
  ACS Synthetic Biology | June 2020, Vol 9(7): pp. 1499-1513
  
  Publication Project
- Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms
  
  Eugene Nadezhdin, Niall Murphy, Neil Dalchau, Andrew Phillips, James C. W. Locke
  
  Nature Communications | February 2020, Vol 11: pp. 950
  
  Publication Project
- Fast enumeration of non-isomorphic chemical reaction networks
  
  Carlo Spaccasassi, Boyan Yordanov, Andrew Phillips, Neil Dalchau
  
  Computational Methods for Systems Biology (CMSB) | September 2019
  
  Editor(s): Luca Bortolussi, Guido Sanguinetti
  
  Author's Version Publication
- Efficient Amortised Bayesian Inference for Hierarchical and Nonlinear Dynamical Systems
  
  Geoffrey Roeder, Paul Grant, Andrew Phillips, Neil Dalchau, Ted Meeds
  
  ICML 2019 | June 2019
  
  Author's Version PDF Project Project
- DNA-based communication in populations of synthetic protocells
  
  Alex Joesaar, Shuo Yang, Bas Bögels, Ardjan van der Linden, Pascal Pieters, B. V. V. S. Pavan Kumar, Neil Dalchau, Andrew Phillips, Stephen Mann, Tom F. A. de Greef
  
  Nature Nanotechnology | March 2019
  
  Publication DOI Project
- A common molecular logic determines embryonic stem cell self-renewal and reprogramming
  
  Sara-Jane Dunn, Meng Amy Li, Elena Carbognin, Austin Smith, Graziano Martello
  
  The EMBO Journal | November 2018, Vol e100003
  
  DOI Publication Project
- A Logic Programming Language for Computational Nucleic Acid Devices
  
  Carlo Spaccasassi, Matthew R. Lakin, Andrew Phillips
  
  ACS Synthetic Biology | October 2018
  
  Publication Project
- Escherichia coli can survive stress by noisy growth modulation
  
  Om Patange, Christian Schwall, Matt Jones, Casandra Villava, Douglas A. Griffith, Andrew Phillips, James C.W. Locke
  
  Nature Communications | September 2018, Vol 53(33)
  
  Publication Project
- Formal Analysis of Network Motifs
  
  Hillel Kugler, Sara-Jane Dunn, Boyan Yordanov
  
  CMSB | September 2018
  
  Publication DOI Project
- Synthesizing and tuning stochastic chemical reaction networks with specified behaviours
  
  Niall Murphy, Rasmus Petersen, Andrew Phillips, Boyan Yordanov, Neil Dalchau
  
  Journal of the Royal Society Interface | August 2018
  
  Publication Publication Project Project
- A Mechanistic Model for Predicting Cell Surface Presentation of Competing Peptides by MHC Class I Molecules
  
  Denise S. M. Boulanger, Ruth C. Eccleston, Andrew Phillips, Peter V. Coveney, T. Elliott, Neil Dalchau
  
  Frontiers in Immunology | July 2018, Vol 9: pp. 1538
  
  Publication Publication Project
- Computing with biological switches and clocks
  
  Neil Dalchau, Gregory Szep, Rosa Hernansaiz-Ballesteros, Chris P Barnes, Luca Cardelli, Andrew Phillips, Attila Csikasz-Nagy
  
  Natural Computing | June 2018
  
  Publication Publication Project Project
- Model reduction enables Turing instability analysis of large reaction–diffusion models
  
  Stephen Smith, Neil Dalchau
  
  Journal of the Royal Society Interface | March 2018, Vol 15
  
  Publication Publication Project
- Predicting DNA hybridization kinetics from sequence
  
  Jinny X. Zhang, John Z. Fang, Wei Duan, Lucia R. Wu, Angela W. Zhang, Neil Dalchau, Boyan Yordanov, Rasmus Petersen, Andrew Phillips, David Yu Zhang
  
  Nature Chemistry | November 2017
  
  Publication Publication Project Project
- Host genotype and time dependent antigen presentation of viral peptides: predictions from theory
  
  Ruth Charlotte Eccleston, Peter V. Coveney, Neil Dalchau
  
  Scientific Reports | October 2017, Vol 7: pp. 14367
  
  Publication Publication Project
- A protein phosphatase network controls the temporal and spatial dynamics of differentiation commitment in human epidermis
  
  Ajay Mishra, Benedicte Oules, Angela Oliveira Pisco, Tony Ly, Kifayathullah Liakath-Ali, Gernot Walko, Priyalakshmi Viswanathan, Matthieu Tihy, Jagdeesh Nijjher, Sara-Jane Dunn, Angus I Lamond, Fiona M Watt
  
  eLife | October 2017, Vol 6:e27356
  
  Publication DOI
- Automated, Constraint-Based Analysis of Tethered DNA Nanostructures
  
  Matthew R. Lakin, Andrew Phillips
  
  International Conference on DNA Computing and Molecular Programming | September 2017
  
  Publication Publication Project
- A spatially localized architecture for fast and modular DNA computing
  
  Gourab Chatterjee, Neil Dalchau, Richard A. Muscat, Andrew Phillips, Georg Seelig
  
  Nature Nanotechnology | July 2017
  
  Publication Publication Project
- The Role of Multiscale Protein Dynamics in Antigen Presentation and T Lymphocyte Recognition
  
  Ruth Charlotte Eccleston, Shunzhou Wan, Neil Dalchau, Peter V. Coveney
  
  Frontiers in Immunology | July 2017
  
  Publication DOI PDF Project
- Efficient Switches in Biology and Computer Science
  
  Luca Cardelli, Rosa D Hernansaiz-Ballesteros, Neil Dalchau, Attila Csikasz-Nagy
  
  PLoS Computational Biology | January 2017, Vol 13: pp. e1005100
  
  Publication Publication Publication
- How computational models contribute to our understanding of the germ line
  
  Kathryn Atwell, Sara-Jane Dunn, James M. Osborne, Hillel Kugler, E. Jane Albert Hubbard
  
  Molecular Reproduction and Development | September 2016
  
  Publication Publication
- A Method to Identify and Analyze Biological Programs through Automated Reasoning
  
  Boyan Yordanov, Sara-Jane Dunn, Hillel Kugler, Austin Smith, Graziano Martello, Stephen Emmott
  
  Systems Biology and Applications | July 2016, Vol 2
  
  Publication Publication
- Algebraic Polynomial-based Synthesis for Abstract Boolean Network Analysis
  
  Peter Backeman, Sara-Jane Dunn, Boyan Yordanov, Christoph M. Wintersteiger, Sara-Jane Dunn, Boyan Yordanov, Christoph M. Wintersteiger
  
  Proceedings of the 14th International Workshop on Satisfiability Modulo Theories (SMT) | July 2016
  
  Publication Project
- A strand graph semantics for DNA-based computation
  
  Rasmus Petersen, Matthew R Lakin, Andrew Phillips
  
  Theoretical Computer Science | June 2016, Vol 632: pp. 43-73
  
  Publication Publication Project
- Modular verification of chemical reaction network encodings via serializability analysis
  
  Matthew R Lakin, Darko Stefanovic, Andrew Phillips
  
  Theoretical Computer Science | June 2016, Vol 632: pp. 21
  
  Publication Project
- Automated Synthesis and Analysis of Switching Gene Regulatory Networks
  
  Yoli Shavit, Boyan Yordanov, Sara-Jane Dunn, Christoph M. Wintersteiger, Tomoki Otani, Frederick J. Livesey, Hillel Kugler
  
  Biosystems | May 2016, Vol 146: pp. 26-34
  
  Publication Publication Publication
- Combined Changes in Wnt Signalling Response and Contact Inhibition Induce Altered Proliferation in Radiation Treated Intestinal Crypts
  
  Sara-Jane Dunn, James M. Osborne, Inke S. Nathke
  
  Molecular Biology of the Cell | April 2016, Vol 27: pp. 1863-1874
  
  Publication Publication
- Computational algorithms as biological switches
  
  Rosa Hernansaiz-Ballesteros, Neil Dalchau, Luca Cardelli, Attila Csikasz-Nagy
  
  Proceedings of the Evry Spring School on Advances in Systems and Synthetic Biology | March 2016
  
  Publication Project
- Noise Reduction in Complex Biological Switches
  
  Attila Csikasz-Nagy, Neil Dalchau, Mirco Tribastone, Max Tschaikowski, Luca Cardelli
  
  Scientific Reports | February 2016, Vol 6: pp. 20214
  
  Publication Publication
- Selector function of MHC I molecules is determined by protein plasticity
  
  Alistair Bailey, Neil Dalchau, Rachel Carter, Stephen Emmott, Andrew Phillips, Jörn M. Werner, Tim Elliott
  
  Scientific Reports | October 2015, Vol 5: pp. 14928
  
  Publication Publication Project
- Characterization of intrinsic properties of promoters
  
  Timothy J. Rudge, James R. Brown, Fernan Federici, Neil Dalchau, Andrew Phillips, James W Ajioka, Jim Haseloff
  
  ACS Synthetic Biology | October 2015
  
  Publication Publication Project
- Synthesizing and tuning chemical reaction networks with specified behaviours
  
  Neil Dalchau, Niall Murphy, Rasmus Petersen, Boyan Yordanov
  
  International Conference on DNA Computing and Molecular Programming | August 2015, Vol 9211
  
  Publication Publication Publication Project
- Probabilistic analysis of localized DNA hybridization circuits
  
  Neil Dalchau, Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif
  
  ACS Synthetic Biology | June 2015, Vol 4: pp. 898-913
  
  Publication Publication Project
- A High-Level Language for Rule-Based Modelling
  
  Michael Pedersen, Andrew Phillips, Gordon D. Plotkin
  
  PLoS ONE | June 2015, Vol 10(6): pp. e0114296
  
  Publication
- Is ‘peak N’ key to understanding the timing of flowering in annual plants?
  
  Camille Guilbaud, Neil Dalchau, Drew Purves, Lindsay Turnbull
  
  New Phytologist | January 2015, Vol 205: pp. 918-927
  
  Publication
- What makes a biological clock efficient?
  
  Attila Csikász-Nagy, Neil Dalchau
  
  MSR-TR-2014-134 | September 2014
  
  Essays for the Luca Cardelli Fest
  
  Publication
- Abstract modelling of tethered DNA circuits
  
  Matthew R. Lakin, Rasmus Petersen, Kathryn E. Gray, Andrew Phillips
  
  International Conference on DNA Computing and Molecular Programming | September 2014
  
  Publication Publication Publication Project
- Computational design of reaction-diffusion patterns using DNA-based chemical reaction networks
  
  Neil Dalchau, Georg Seelig, Andrew Phillips
  
  International Conference on DNA Computing and Molecular Programming | September 2014
  
  Publication Publication Publication Project
- Understanding and predicting biological networks using linear system identification
  
  Alberto Carignano, Ye Yuan, Neil Dalchau, Alex AR Webb, Jorge M Goncalves
  
  A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations, 9 | Published by Springer | 2014 | A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations edition
  
  Publication Publication
- Analyzing and Synthesizing Genomic Logic Functions
  
  Nicola Paoletti, Boyan Yordanov, Youssef Hamadi, Christoph M. Wintersteiger, Hillel Kugler
  
  26th International Conference on Computer Aided Verification (CAV) | July 2014
  
  Publication Publication Publication Project
- Computational design of nucleic acid feedback control circuits
  
  Boyan Yordanov, Jongmin Kim, Rasmus L. Petersen, Angelina Shudy, Vishwesh V. Kulkarni, Andrew Phillips
  
  ACS Synthetic Biology | July 2014, Vol 3: pp. 600-616
  
  Publication Publication Project
- Defining an essential transcriptional factor program for naive pluripotency
  
  Sara-Jane Dunn, Graziano Martello, Boyan Yordanov, Stephen Emmott, Austin Smith
  
  Science | June 2014, Vol 344: pp. 1156
  
  Publication Project
- A Computational Method for Automated Characterization of Genetic Components
  
  Neil Dalchau, Boyan Yordanov, Paul Grant, Michael Pedersen, Stephen Emmott, Jim Haseloff, Andrew Phillips
  
  ACS Synthetic Biology | March 2014, Vol 3(8): pp. 578-588
  
  Publication Publication Project
- Ten Simple Rules for Effective Computational Research
  
  James Osborne, Miguel Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander Fletcher, Derek Groen, Bernhard Knapp, Gary Mirams, Joe Pitt-Francis, Biswa Sengupta, David Wright, Christian Yates, David Gavaghan, Stephen Emmott, Charlotte Deane
  
  PLoS Computational Biology | March 2014, pp. e1003506
  
  Publication
- Bio Simulators: a web UI for biological simulation
  
  Michael Pedersen, Nicolas Oury, Andrew Phillips
  
  Bioinformatics | January 2014, Vol 30: pp. 1491-1492
  
  Publication Publication
- Compiling DNA Strand Displacement Reactions Using a Functional Programming Language
  
  Matthew R Lakin, Andrew Phillips
  
  Practical Aspects of Declarative Languages - 16th International Symposium | January 2014
  
  Publication Project
- Biocharts: Unifying Biological Hypotheses with Models and Experiments
  
  Hillel Kugler
  
  IEEE 9th International Conference on e-Science | October 2013
  
  Publication
- Programmable chemical controllers made from DNA
  
  Yuan-Jyue Chen, Neil Dalchau, Niranjan Srnivas, Andrew Phillips, Luca Cardelli, David Soloveichik, Georg Seelig
  
  Nature Nanotechnology | September 2013, Vol 8: pp. 755-762
  
  Publication Project
- The circadian clock has transient plasticity of period and is required for timing of nocturnal processes in Arabidopsis
  
  Antony N Dodd, Neil Dalchau, Michael J Gardner, Seong Jin Baek, Alex AR Webb
  
  New Phytologist | September 2013, Vol 201(1): pp. 168-179
  
  Publication
- Functional Analysis of Large-scale DNA Strand Displacement Circuits
  
  Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, Andrew Phillips, Hillel Kugler
  
  International Conference on DNA Computing and Molecular Programming | September 2013
  
  Publication Publication Project Project
- Modular verification of DNA strand displacement networks via serializability analysis
  
  Matthew R. Lakin, Andrew Phillips, Darko Stefanovic
  
  International Conference on DNA Computing and Molecular Programming | September 2013, Vol 8141: pp. 133-146
  
  Publication Publication Publication Project
- Automated Ratiometric Characterization using GEC
  
  Paul Grant, Jim Haseloff, Stephen Emmott, Boyan Yordanov, Neil Dalchau, Andrew Phillips
  
  International Workshop on Biodesign Automation | July 2013
  
  Publication Project
- Z34Bio: An SMT-based Framework for Analyzing Biological Computation
  
  Boyan Yordanov, Youssef Hamadi, Hillel Kugler, Christoph M. Wintersteiger
  
  SMT'13 | July 2013
  
  Publication Project
- SMT-based Analysis of Biological Computation
  
  Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, Hillel Kugler
  
  NASA Formal Methods Symposium 2013 | May 2013
  
  Publication Project
- Chaste: An Open Source C++ Library for Computational Physiology and Biology
  
  G. R. Mirams, C. J. Arthurs, M. O. Bernabeu, R. Bordas, J. Cooper, A. Corrias, Y. Davit, Sara-Jane Dunn, A. G. Fletcher, D. G. Harvey, M. E. Marsh, J. M. Osborne, P. Pathmanathan, J. Pitt-Francis, J. Southern, N. Zemzemi, D. J. Gavaghan
  
  PLOS Comput. Biol. | March 2013
  
  Publication
- Oligodendrocyte dynamics in the healthy adult CNS: evidence for myelin remodelling
  
  Kaylene M. Young, Konstantina Psachoulia, Richa B. Tripathi, Sara-Jane Dunn, Lee Cossell, David Attwell, Koujiro Tohyama, William D. Richardson
  
  Neuron | March 2013
  
  Publication
- Computational Modeling of Synthetic Microbial Biofilms
  
  Timothy J. Rudge, Paul J. Steiner, Andrew Phillips, Jim Haseloff
  
  ACS Synthetic Biology | July 2012, Vol 1: pp. 345-352
  
  Publication Project
- Design and Analysis of DNA Strand Displacement Devices using Probabilistic Model Checking
  
  Matthew R. Lakin,, David Parker, Luca Cardelli, Marta Kwiatkowska, Andrew Phillips
  
  Journal of the Royal Society Interface | July 2012, Vol 9: pp. 1470-1485
  
  Publication Project
- A Two-Dimensional Model of the Colonic Crypt Accounting for the Role of the Basement Membrane and Pericryptal Fibroblast Sheath
  
  Sara-Jane Dunn, Paul L. Appleton, Scott A. Nelson, Inke S. Nathke, David J. Gavaghan, James M. Osborne
  
  PLoS Computational Biology | May 2012
  
  Publication
- Stochastic Simulation of Multiple Process Calculi for Biology
  
  Matthew R. Lakin, Loïc Paulevé, Andrew Phillips
  
  Theoretical Computer Science | May 2012, Vol 431: pp. 181-206
  
  Publication Publication Project Project
- Towards the rational design of synthetic cells with prescribed population dynamics
  
  Neil Dalchau, Matthew Smith, Samuel Martin, James R Brown, Stephen Emmott, Andrew Phillips
  
  Journal of the Royal Society Interface | May 2012, Vol 9: pp. 2883-2898
  
  Publication Project
- Z3-4Biology SMT-Based Analysis of Biological Computation
  
  Boyan Yordanov, Youssef Hamadi, Hillel Kugler, Christoph M. Wintersteiger
  
  MSR-TR-2012-31 | March 2012
  
  Publication Project
- Abstractions for DNA circuit design
  
  Matthew R Lakin, Simon Youssef, Luca Cardelli, Andrew Phillips
  
  Journal of the Royal Society Interface | March 2012, Vol 9(68): pp. 470-486
  
  Publication Publication Project
- Understanding biological timing using mechanistic and black-box models
  
  Neil Dalchau
  
  New Phytologist | March 2012, Vol 193(4): pp. 852-858
  
  Publication
- A model of stem cell population dynamics: in-silico analysis and in-vivo validation
  
  Hillel Kugler
  
  Development | January 2012, Vol 139: pp. 47
  
  Publication Publication Publication
- Modelling the role of the basement membrane beneath a growing epithelial monolayer
  
  Sara-Jane Dunn, Alexander G. Fletcher, S. Jonathan Chapman, David J. Gavaghan, James M. Osborne
  
  Journal of Theoretical Biology | December 2011
  
  Publication
- Visual DSD: a design and analysis tool for DNA strand displacement systems
  
  Matthew R Lakin, Simon Youssef, Filippo Polo, Stephen Emmott, Andrew Phillips
  
  Bioinformatics | November 2011, Vol 27: pp. 3211-3213
  
  Publication Project
- A peptide filtering relation quantifies MHC class I peptide optimization
  
  Neil Dalchau, Andrew Phillips, Leonard D Goldstein, Mark Howarth, Luca Cardelli, Stephen Emmott, Tim Elliott, Joern M Werner
  
  PLoS Computational Biology | October 2011, Vol 7(10): pp. e1002144
  
  Publication Publication Project Project
- How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex
  
  Yaki Setty, Chih-Chun Chen, Maria Secrier, Nikita Skoblov, Dimitrios Kalamatianos, Stephen Emmott
  
  BMC Systems Biology | September 2011
  
  Publication
- Localized Hybridization Circuits
  
  Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif
  
  International Conference on DNA Computing and Molecular Programming | September 2011, Vol 6937: pp. 64-83
  
  Publication Publication Publication Project
- Modelling, simulating and verifying Turing-powerful strand displacement systems
  
  Andrew Phillips, Matthew R Lakin
  
  International Conference on DNA Computing and Molecular Programming | September 2011
  
  Publication DOI Project
- Synthesizing Biological Theories
  
  Hillel Kugler, Cory Plock, Andy Roberts
  
  Computer Aided Verification (CAV'11) | July 2011
  
  Publication Download
- Model Checking Using SMT and Theory of Lists
  
  Aleksandar Milicevic, Hillel Kugler
  
  Nasa Formal Methods Symposium | April 2011
  
  Nasa Formal Methods Symposium
  
  Publication Publication
- The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose
  
  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, Alex AR Webb
  
  Proceedings of the National Academy of Sciences | March 2011
  
  Publication
- Ticking Over – Circadian Systems Across the Kingdoms of Life
  
  Neil Dalchau, Alex AR Webb
  
  Biochemist | February 2011, Vol 33(1): pp. 12-15
  
  Publication
- Stochastic Simulation of Process Calculi for Biology
  
  Andrew Phillips, Matthew R. Lakin, Loïc Paulevé
  
  Electronic Proceedings in Theoretical Computer Science | November 2010
  
  Publication Publication Project
- The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding
  
  Andy van Hateren, Ed James, Alistair Bailey, Andrew Phillips, Neil Dalchau, Tim Elliott
  
  Tissue Antigens | October 2010, Vol 76(4): pp. 259
  
  Publication Publication Project
- A Generic Abstract Machine for Stochastic Process Calculi
  
  Loïc Paulevé, Simon Youssef, Matthew R. Lakin, Andrew Phillips
  
  Computational Methods in Systems Biology | September 2010, pp. 43-54
  
  Publication Publication Project
- Modeling Alveolar Volume Changes During Periodic Breathing in Heterogeneously Ventilated Lungs
  
  Sara-Jane Dunn, Jonathan P. Whiteley
  
  Annals of Biomedical Engineering | September 2010, Vol 38: pp. 2988-2999
  
  Publication Publication
- Biocharts: A Visual Formalism for Complex Biological Systems
  
  Hillel Kugler, Antti Larjo, David Harel
  
  Journal of the Royal Society Interface | July 2010, Vol 7: pp. 1015-1024
  
  Published online December 2009
  
  Publication Publication
- Correct biological timing in Arabidopsis requires multiple light signaling pathways
  
  Neil Dalchau, Katharine E Hubbard, Fiona C Robertson, Carlos T Hotta, Helen M Briggs, Guy-Bart Stan, Jorge M Goncalves, Alex A R Webb
  
  Proceedings of the National Academy of Sciences | July 2010
  
  Publication
- The Neuroepithelial Basement Membrane Serves As A Boundary And A Substrate For Neuron Migration In The Zebrafish Hindbrain
  
  Paul Grant, Cecilia Moens
  
  Neural Development | March 2010, Vol 5
  
  Publication Publication Publication
- Accelerating Smart Play-Out
  
  David Harel, Hillel Kugler, Shahar Maoz, Itai Segali
  
  SOFSEM 2010: Theory and Practice of Computer Science | January 2010
  
  Publication Publication
- Disruption of two defensive signaling pathways by a viral RNA silencing suppressor
  
  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, John P Carr
  
  Molecular Plant-Microbe Interations | January 2010, Vol 23: pp. 835-845
  
  Publication
- Some Thoughts on the Semantics of Biocharts
  
  David Harel, Hillel Kugler
  
  Essays in Memory of Amir Pnueli | January 2010
  
  Dedicated to the dear memory of Amir Pnueli: Friend, mentor, colleague, and a truly towering figure in computer science
  
  Publication Publication
- Computational Modeling of the EGFR Network Elucidates Control Mechanisms Regulating Signal Dynamics
  
  Dennis YQ Wang, Luca Cardelli, Andrew Phillips, Nir Piterman, Jasmin Fisher
  
  BMC Systems Biology | December 2009, Vol 3: pp. 118
  
  Publication Project
- A Process Model of Rho GTP-binding Proteins
  
  Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanogullari, Andrew Phillips
  
  Theoretical Computer Science | August 2009, Vol 410: pp. 3166-3185
  
  Publication Publication Project
- Systems analyses of circadian networks
  
  Katharine E. Hubbard, Fiona C. Robertson, Neil Dalchau, Alex A. R. Webb
  
  Molecular Biosystems | August 2009, Vol 5: pp. 1502-1511
  
  Publication Publication
- A programming language for composable DNA circuits
  
  Andrew Phillips, Luca Cardelli
  
  Journal of the Royal Society Interface | June 2009, Vol 6: pp. S419-S436
  
  Publication Publication Project
- Towards programming languages for genetic engineering of living cells
  
  Michael Pedersen, Andrew Phillips
  
  Journal of the Royal Society Interface | April 2009, Vol 6: pp. S437-S450
  
  Publication Publication Publication Project
- Compositional Synthesis of Reactive Systems from Live Sequence Chart Specifications
  
  Hillel Kugler
  
  Tools and Algorithms for the Construction and Analysis of Systems (TACAS'09) | March 2009
  
  Publication Publication
- Controller Synthesis from LSC Requirements
  
  Hillel Kugler, Cory Plock, Amir Pnueli
  
  Fundamental Approaches to Software Engineering (FASE'09) | March 2009
  
  Publication Publication
- A Process Model of Actin Polymerisation
  
  Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanoğulları, Andrew Phillips
  
  Electronic Notes in Theoretical Computer Science | February 2009, Vol 229(1): pp. 127-144
  
  Publication Publication Project
- A Visual Process Calculus for Biology
  
  Andrew Phillips
  
  Symbolic Systems Biology: Theory and Methods | Published by Jones and Bartlett Publishers | 2009 | Symbolic Systems Biology: Theory and Methods edition
  
  Publication Project
- An Abstract Machine for the Stochastic Bioambient Calculus
  
  Andrew Phillips
  
  Electronic Notes in Theoretical Computer Science | January 2009, Vol 227: pp. 143-159
  
  Publication Publication Project
- How Hard is Smart Play-Out? On the Complexity of Verification-Driven Execution
  
  David Harel, Hillel Kugler, Shahar Maoz, Itai Segall
  
  Perspectives in Concurrency Theory (Festschrift for P.S. Thiagarajan), (K. Lodaya et al, eds.), University Press (India) | January 2009
  
  Perspectives in Concurrency Theory (Festschrift for P.S. Thiagarajan), (K. Lodaya et al, eds.), University Press (India)
  
  Publication

- A deep learning model for predicting next-generation sequencing depth from DNA sequence
  
  Jinny X. Zhang, Boyan Yordanov, Alexander Gaunt, Michael X. Wang, Peng Dai, Yuan-Jyue Chen, Kerou Zhang, John Z. Fang, Neil Dalchau, Jiaming Li, Andrew Phillips, David Yu Zhang
  
  Nature Communications | July 2021, Vol 12
  
  Publication Project
- Efficient Amortised Bayesian Inference for Hierarchical and Nonlinear Dynamical Systems
  
  Geoffrey Roeder, Paul Grant, Andrew Phillips, Neil Dalchau, Ted Meeds
  
  ICML 2019 | June 2019
  
  Author's Version PDF Project Project
- A deep learning model for predicting next-generation sequencing depth from DNA sequence
  
  Jinny X. Zhang, Boyan Yordanov, Alexander Gaunt, Michael X. Wang, Peng Dai, Yuan-Jyue Chen, Kerou Zhang, John Z. Fang, Neil Dalchau, Jiaming Li, Andrew Phillips, David Yu Zhang
  
  Nature Communications | July 2021, Vol 12
  
  Publication Project
- A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction.
  
  Trevor Y. H. Ho, Alexander Shao, Zeyu Lu, Harri Savilahti, Filippo Menolascina, Lei Wang, Neil Dalchau, Baojun Wang
  
  Nature Communications | April 2021, Vol 12(1): pp. 2200-2200
  
  DOI Publication
- Interpretation of morphogen gradients by a synthetic bistable circuit
  
  Paul Grant, Gregory Szep, Om Patange, Jacob Halatek, Valerie Coppard, Attila Csikasz-Nagy, Jim Haseloff, James C. W. Locke, Neil Dalchau, Andrew Phillips
  
  Nature Communications | November 2020, Vol 11(5545)
  
  Publication Project
- Domain-specific programming languages for computational nucleic acid systems
  
  Matthew R. Lakin, Andrew Phillips
  
  ACS Synthetic Biology | June 2020, Vol 9(7): pp. 1499-1513
  
  Publication Project
- Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms
  
  Eugene Nadezhdin, Niall Murphy, Neil Dalchau, Andrew Phillips, James C. W. Locke
  
  Nature Communications | February 2020, Vol 11: pp. 950
  
  Publication Project
- DNA-based communication in populations of synthetic protocells
  
  Alex Joesaar, Shuo Yang, Bas Bögels, Ardjan van der Linden, Pascal Pieters, B. V. V. S. Pavan Kumar, Neil Dalchau, Andrew Phillips, Stephen Mann, Tom F. A. de Greef
  
  Nature Nanotechnology | March 2019
  
  Publication DOI Project
- A common molecular logic determines embryonic stem cell self-renewal and reprogramming
  
  Sara-Jane Dunn, Meng Amy Li, Elena Carbognin, Austin Smith, Graziano Martello
  
  The EMBO Journal | November 2018, Vol e100003
  
  DOI Publication Project
- A Logic Programming Language for Computational Nucleic Acid Devices
  
  Carlo Spaccasassi, Matthew R. Lakin, Andrew Phillips
  
  ACS Synthetic Biology | October 2018
  
  Publication Project
- Escherichia coli can survive stress by noisy growth modulation
  
  Om Patange, Christian Schwall, Matt Jones, Casandra Villava, Douglas A. Griffith, Andrew Phillips, James C.W. Locke
  
  Nature Communications | September 2018, Vol 53(33)
  
  Publication Project
- Formal Analysis of Network Motifs
  
  Hillel Kugler, Sara-Jane Dunn, Boyan Yordanov
  
  CMSB | September 2018
  
  Publication DOI Project
- A Mechanistic Model for Predicting Cell Surface Presentation of Competing Peptides by MHC Class I Molecules
  
  Denise S. M. Boulanger, Ruth C. Eccleston, Andrew Phillips, Peter V. Coveney, T. Elliott, Neil Dalchau
  
  Frontiers in Immunology | July 2018, Vol 9: pp. 1538
  
  Publication Publication Project
- Predicting DNA hybridization kinetics from sequence
  
  Jinny X. Zhang, John Z. Fang, Wei Duan, Lucia R. Wu, Angela W. Zhang, Neil Dalchau, Boyan Yordanov, Rasmus Petersen, Andrew Phillips, David Yu Zhang
  
  Nature Chemistry | November 2017
  
  Publication Publication Project Project
- Host genotype and time dependent antigen presentation of viral peptides: predictions from theory
  
  Ruth Charlotte Eccleston, Peter V. Coveney, Neil Dalchau
  
  Scientific Reports | October 2017, Vol 7: pp. 14367
  
  Publication Publication Project
- A protein phosphatase network controls the temporal and spatial dynamics of differentiation commitment in human epidermis
  
  Ajay Mishra, Benedicte Oules, Angela Oliveira Pisco, Tony Ly, Kifayathullah Liakath-Ali, Gernot Walko, Priyalakshmi Viswanathan, Matthieu Tihy, Jagdeesh Nijjher, Sara-Jane Dunn, Angus I Lamond, Fiona M Watt
  
  eLife | October 2017, Vol 6:e27356
  
  Publication DOI
- Automated, Constraint-Based Analysis of Tethered DNA Nanostructures
  
  Matthew R. Lakin, Andrew Phillips
  
  International Conference on DNA Computing and Molecular Programming | September 2017
  
  Publication Publication Project
- A spatially localized architecture for fast and modular DNA computing
  
  Gourab Chatterjee, Neil Dalchau, Richard A. Muscat, Andrew Phillips, Georg Seelig
  
  Nature Nanotechnology | July 2017
  
  Publication Publication Project
- The Role of Multiscale Protein Dynamics in Antigen Presentation and T Lymphocyte Recognition
  
  Ruth Charlotte Eccleston, Shunzhou Wan, Neil Dalchau, Peter V. Coveney
  
  Frontiers in Immunology | July 2017
  
  Publication DOI PDF Project
- Efficient Switches in Biology and Computer Science
  
  Luca Cardelli, Rosa D Hernansaiz-Ballesteros, Neil Dalchau, Attila Csikasz-Nagy
  
  PLoS Computational Biology | January 2017, Vol 13: pp. e1005100
  
  Publication Publication Publication
- How computational models contribute to our understanding of the germ line
  
  Kathryn Atwell, Sara-Jane Dunn, James M. Osborne, Hillel Kugler, E. Jane Albert Hubbard
  
  Molecular Reproduction and Development | September 2016
  
  Publication Publication
- A Method to Identify and Analyze Biological Programs through Automated Reasoning
  
  Boyan Yordanov, Sara-Jane Dunn, Hillel Kugler, Austin Smith, Graziano Martello, Stephen Emmott
  
  Systems Biology and Applications | July 2016, Vol 2
  
  Publication Publication
- Algebraic Polynomial-based Synthesis for Abstract Boolean Network Analysis
  
  Peter Backeman, Sara-Jane Dunn, Boyan Yordanov, Christoph M. Wintersteiger, Sara-Jane Dunn, Boyan Yordanov, Christoph M. Wintersteiger
  
  Proceedings of the 14th International Workshop on Satisfiability Modulo Theories (SMT) | July 2016
  
  Publication Project
- Automated Synthesis and Analysis of Switching Gene Regulatory Networks
  
  Yoli Shavit, Boyan Yordanov, Sara-Jane Dunn, Christoph M. Wintersteiger, Tomoki Otani, Frederick J. Livesey, Hillel Kugler
  
  Biosystems | May 2016, Vol 146: pp. 26-34
  
  Publication Publication Publication
- Combined Changes in Wnt Signalling Response and Contact Inhibition Induce Altered Proliferation in Radiation Treated Intestinal Crypts
  
  Sara-Jane Dunn, James M. Osborne, Inke S. Nathke
  
  Molecular Biology of the Cell | April 2016, Vol 27: pp. 1863-1874
  
  Publication Publication
- Understanding and predicting biological networks using linear system identification
  
  Alberto Carignano, Ye Yuan, Neil Dalchau, Alex AR Webb, Jorge M Goncalves
  
  A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations, 9 | Published by Springer | 2014 | A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations edition
  
  Publication Publication
- Analyzing and Synthesizing Genomic Logic Functions
  
  Nicola Paoletti, Boyan Yordanov, Youssef Hamadi, Christoph M. Wintersteiger, Hillel Kugler
  
  26th International Conference on Computer Aided Verification (CAV) | July 2014
  
  Publication Publication Publication Project
- Ten Simple Rules for Effective Computational Research
  
  James Osborne, Miguel Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander Fletcher, Derek Groen, Bernhard Knapp, Gary Mirams, Joe Pitt-Francis, Biswa Sengupta, David Wright, Christian Yates, David Gavaghan, Stephen Emmott, Charlotte Deane
  
  PLoS Computational Biology | March 2014, pp. e1003506
  
  Publication
- Biocharts: Unifying Biological Hypotheses with Models and Experiments
  
  Hillel Kugler
  
  IEEE 9th International Conference on e-Science | October 2013
  
  Publication
- Z34Bio: An SMT-based Framework for Analyzing Biological Computation
  
  Boyan Yordanov, Youssef Hamadi, Hillel Kugler, Christoph M. Wintersteiger
  
  SMT'13 | July 2013
  
  Publication Project
- SMT-based Analysis of Biological Computation
  
  Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, Hillel Kugler
  
  NASA Formal Methods Symposium 2013 | May 2013
  
  Publication Project
- Chaste: An Open Source C++ Library for Computational Physiology and Biology
  
  G. R. Mirams, C. J. Arthurs, M. O. Bernabeu, R. Bordas, J. Cooper, A. Corrias, Y. Davit, Sara-Jane Dunn, A. G. Fletcher, D. G. Harvey, M. E. Marsh, J. M. Osborne, P. Pathmanathan, J. Pitt-Francis, J. Southern, N. Zemzemi, D. J. Gavaghan
  
  PLOS Comput. Biol. | March 2013
  
  Publication
- Oligodendrocyte dynamics in the healthy adult CNS: evidence for myelin remodelling
  
  Kaylene M. Young, Konstantina Psachoulia, Richa B. Tripathi, Sara-Jane Dunn, Lee Cossell, David Attwell, Koujiro Tohyama, William D. Richardson
  
  Neuron | March 2013
  
  Publication
- A Two-Dimensional Model of the Colonic Crypt Accounting for the Role of the Basement Membrane and Pericryptal Fibroblast Sheath
  
  Sara-Jane Dunn, Paul L. Appleton, Scott A. Nelson, Inke S. Nathke, David J. Gavaghan, James M. Osborne
  
  PLoS Computational Biology | May 2012
  
  Publication
- Z3-4Biology SMT-Based Analysis of Biological Computation
  
  Boyan Yordanov, Youssef Hamadi, Hillel Kugler, Christoph M. Wintersteiger
  
  MSR-TR-2012-31 | March 2012
  
  Publication Project
- A model of stem cell population dynamics: in-silico analysis and in-vivo validation
  
  Hillel Kugler
  
  Development | January 2012, Vol 139: pp. 47
  
  Publication Publication Publication
- Modelling the role of the basement membrane beneath a growing epithelial monolayer
  
  Sara-Jane Dunn, Alexander G. Fletcher, S. Jonathan Chapman, David J. Gavaghan, James M. Osborne
  
  Journal of Theoretical Biology | December 2011
  
  Publication
- How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex
  
  Yaki Setty, Chih-Chun Chen, Maria Secrier, Nikita Skoblov, Dimitrios Kalamatianos, Stephen Emmott
  
  BMC Systems Biology | September 2011
  
  Publication
- Synthesizing Biological Theories
  
  Hillel Kugler, Cory Plock, Andy Roberts
  
  Computer Aided Verification (CAV'11) | July 2011
  
  Publication Download
- The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding
  
  Andy van Hateren, Ed James, Alistair Bailey, Andrew Phillips, Neil Dalchau, Tim Elliott
  
  Tissue Antigens | October 2010, Vol 76(4): pp. 259
  
  Publication Publication Project
- Modeling Alveolar Volume Changes During Periodic Breathing in Heterogeneously Ventilated Lungs
  
  Sara-Jane Dunn, Jonathan P. Whiteley
  
  Annals of Biomedical Engineering | September 2010, Vol 38: pp. 2988-2999
  
  Publication Publication
- Biocharts: A Visual Formalism for Complex Biological Systems
  
  Hillel Kugler, Antti Larjo, David Harel
  
  Journal of the Royal Society Interface | July 2010, Vol 7: pp. 1015-1024
  
  Published online December 2009
  
  Publication Publication
- The Neuroepithelial Basement Membrane Serves As A Boundary And A Substrate For Neuron Migration In The Zebrafish Hindbrain
  
  Paul Grant, Cecilia Moens
  
  Neural Development | March 2010, Vol 5
  
  Publication Publication Publication
- Some Thoughts on the Semantics of Biocharts
  
  David Harel, Hillel Kugler
  
  Essays in Memory of Amir Pnueli | January 2010
  
  Dedicated to the dear memory of Amir Pnueli: Friend, mentor, colleague, and a truly towering figure in computer science
  
  Publication Publication
- Computational Modeling of the EGFR Network Elucidates Control Mechanisms Regulating Signal Dynamics
  
  Dennis YQ Wang, Luca Cardelli, Andrew Phillips, Nir Piterman, Jasmin Fisher
  
  BMC Systems Biology | December 2009, Vol 3: pp. 118
  
  Publication Project
- Controller Synthesis from LSC Requirements
  
  Hillel Kugler, Cory Plock, Amir Pnueli
  
  Fundamental Approaches to Software Engineering (FASE'09) | March 2009
  
  Publication Publication
- Compositional Synthesis of Reactive Systems from Live Sequence Chart Specifications
  
  Hillel Kugler
  
  Tools and Algorithms for the Construction and Analysis of Systems (TACAS'09) | March 2009
  
  Publication Publication
- Interpretation of morphogen gradients by a synthetic bistable circuit
  
  Paul Grant, Gregory Szep, Om Patange, Jacob Halatek, Valerie Coppard, Attila Csikasz-Nagy, Jim Haseloff, James C. W. Locke, Neil Dalchau, Andrew Phillips
  
  Nature Communications | November 2020, Vol 11(5545)
  
  Publication Project
- Automated, Constraint-Based Analysis of Tethered DNA Nanostructures
  
  Matthew R. Lakin, Andrew Phillips
  
  International Conference on DNA Computing and Molecular Programming | September 2017
  
  Publication Publication Project
- Noise Reduction in Complex Biological Switches
  
  Attila Csikasz-Nagy, Neil Dalchau, Mirco Tribastone, Max Tschaikowski, Luca Cardelli
  
  Scientific Reports | February 2016, Vol 6: pp. 20214
  
  Publication Publication
- Analyzing and Synthesizing Genomic Logic Functions
  
  Nicola Paoletti, Boyan Yordanov, Youssef Hamadi, Christoph M. Wintersteiger, Hillel Kugler
  
  26th International Conference on Computer Aided Verification (CAV) | July 2014
  
  Publication Publication Publication Project
- Functional Analysis of Large-scale DNA Strand Displacement Circuits
  
  Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, Andrew Phillips, Hillel Kugler
  
  International Conference on DNA Computing and Molecular Programming | September 2013
  
  Publication Publication Project Project
- Model Checking Using SMT and Theory of Lists
  
  Aleksandar Milicevic, Hillel Kugler
  
  Nasa Formal Methods Symposium | April 2011
  
  Nasa Formal Methods Symposium
  
  Publication Publication
- Stochastic Simulation of Process Calculi for Biology
  
  Andrew Phillips, Matthew R. Lakin, Loïc Paulevé
  
  Electronic Proceedings in Theoretical Computer Science | November 2010
  
  Publication Publication Project
- Accelerating Smart Play-Out
  
  David Harel, Hillel Kugler, Shahar Maoz, Itai Segali
  
  SOFSEM 2010: Theory and Practice of Computer Science | January 2010
  
  Publication Publication
- A programming language for composable DNA circuits
  
  Andrew Phillips, Luca Cardelli
  
  Journal of the Royal Society Interface | June 2009, Vol 6: pp. S419-S436
  
  Publication Publication Project
- How Hard is Smart Play-Out? On the Complexity of Verification-Driven Execution
  
  David Harel, Hillel Kugler, Shahar Maoz, Itai Segall
  
  Perspectives in Concurrency Theory (Festschrift for P.S. Thiagarajan), (K. Lodaya et al, eds.), University Press (India) | January 2009
  
  Perspectives in Concurrency Theory (Festschrift for P.S. Thiagarajan), (K. Lodaya et al, eds.), University Press (India)
  
  Publication
- Turing Patterning in Stratified Domains
  
  Andrew L. Krause, Vaclav Klika, Jacob Halatek, Paul Grant, Thomas L. Woolley, Neil Dalchau, Eamonn A. Gaffney
  
  Bulletin of Mathematical Biology | October 2020, Vol 82(136)
  
  Publication Publication Project
- Synthesizing and tuning stochastic chemical reaction networks with specified behaviours
  
  Niall Murphy, Rasmus Petersen, Andrew Phillips, Boyan Yordanov, Neil Dalchau
  
  Journal of the Royal Society Interface | August 2018
  
  Publication Publication Project Project
- Model reduction enables Turing instability analysis of large reaction–diffusion models
  
  Stephen Smith, Neil Dalchau
  
  Journal of the Royal Society Interface | March 2018, Vol 15
  
  Publication Publication Project
- A strand graph semantics for DNA-based computation
  
  Rasmus Petersen, Matthew R Lakin, Andrew Phillips
  
  Theoretical Computer Science | June 2016, Vol 632: pp. 43-73
  
  Publication Publication Project
- Modular verification of chemical reaction network encodings via serializability analysis
  
  Matthew R Lakin, Darko Stefanovic, Andrew Phillips
  
  Theoretical Computer Science | June 2016, Vol 632: pp. 21
  
  Publication Project
- Automated Synthesis and Analysis of Switching Gene Regulatory Networks
  
  Yoli Shavit, Boyan Yordanov, Sara-Jane Dunn, Christoph M. Wintersteiger, Tomoki Otani, Frederick J. Livesey, Hillel Kugler
  
  Biosystems | May 2016, Vol 146: pp. 26-34
  
  Publication Publication Publication
- Computational algorithms as biological switches
  
  Rosa Hernansaiz-Ballesteros, Neil Dalchau, Luca Cardelli, Attila Csikasz-Nagy
  
  Proceedings of the Evry Spring School on Advances in Systems and Synthetic Biology | March 2016
  
  Publication Project
- Noise Reduction in Complex Biological Switches
  
  Attila Csikasz-Nagy, Neil Dalchau, Mirco Tribastone, Max Tschaikowski, Luca Cardelli
  
  Scientific Reports | February 2016, Vol 6: pp. 20214
  
  Publication Publication
- Selector function of MHC I molecules is determined by protein plasticity
  
  Alistair Bailey, Neil Dalchau, Rachel Carter, Stephen Emmott, Andrew Phillips, Jörn M. Werner, Tim Elliott
  
  Scientific Reports | October 2015, Vol 5: pp. 14928
  
  Publication Publication Project
- Characterization of intrinsic properties of promoters
  
  Timothy J. Rudge, James R. Brown, Fernan Federici, Neil Dalchau, Andrew Phillips, James W Ajioka, Jim Haseloff
  
  ACS Synthetic Biology | October 2015
  
  Publication Publication Project
- Synthesizing and tuning chemical reaction networks with specified behaviours
  
  Neil Dalchau, Niall Murphy, Rasmus Petersen, Boyan Yordanov
  
  International Conference on DNA Computing and Molecular Programming | August 2015, Vol 9211
  
  Publication Publication Publication Project
- Probabilistic analysis of localized DNA hybridization circuits
  
  Neil Dalchau, Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif
  
  ACS Synthetic Biology | June 2015, Vol 4: pp. 898-913
  
  Publication Publication Project
- A High-Level Language for Rule-Based Modelling
  
  Michael Pedersen, Andrew Phillips, Gordon D. Plotkin
  
  PLoS ONE | June 2015, Vol 10(6): pp. e0114296
  
  Publication
- Is ‘peak N’ key to understanding the timing of flowering in annual plants?
  
  Camille Guilbaud, Neil Dalchau, Drew Purves, Lindsay Turnbull
  
  New Phytologist | January 2015, Vol 205: pp. 918-927
  
  Publication
- What makes a biological clock efficient?
  
  Attila Csikász-Nagy, Neil Dalchau
  
  MSR-TR-2014-134 | September 2014
  
  Essays for the Luca Cardelli Fest
  
  Publication
- Computational design of reaction-diffusion patterns using DNA-based chemical reaction networks
  
  Neil Dalchau, Georg Seelig, Andrew Phillips
  
  International Conference on DNA Computing and Molecular Programming | September 2014
  
  Publication Publication Publication Project
- Abstract modelling of tethered DNA circuits
  
  Matthew R. Lakin, Rasmus Petersen, Kathryn E. Gray, Andrew Phillips
  
  International Conference on DNA Computing and Molecular Programming | September 2014
  
  Publication Publication Publication Project
- Understanding and predicting biological networks using linear system identification
  
  Alberto Carignano, Ye Yuan, Neil Dalchau, Alex AR Webb, Jorge M Goncalves
  
  A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations, 9 | Published by Springer | 2014 | A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations edition
  
  Publication Publication
- Analyzing and Synthesizing Genomic Logic Functions
  
  Nicola Paoletti, Boyan Yordanov, Youssef Hamadi, Christoph M. Wintersteiger, Hillel Kugler
  
  26th International Conference on Computer Aided Verification (CAV) | July 2014
  
  Publication Publication Publication Project
- Computational design of nucleic acid feedback control circuits
  
  Boyan Yordanov, Jongmin Kim, Rasmus L. Petersen, Angelina Shudy, Vishwesh V. Kulkarni, Andrew Phillips
  
  ACS Synthetic Biology | July 2014, Vol 3: pp. 600-616
  
  Publication Publication Project
- Defining an essential transcriptional factor program for naive pluripotency
  
  Sara-Jane Dunn, Graziano Martello, Boyan Yordanov, Stephen Emmott, Austin Smith
  
  Science | June 2014, Vol 344: pp. 1156
  
  Publication Project
- A Computational Method for Automated Characterization of Genetic Components
  
  Neil Dalchau, Boyan Yordanov, Paul Grant, Michael Pedersen, Stephen Emmott, Jim Haseloff, Andrew Phillips
  
  ACS Synthetic Biology | March 2014, Vol 3(8): pp. 578-588
  
  Publication Publication Project
- Bio Simulators: a web UI for biological simulation
  
  Michael Pedersen, Nicolas Oury, Andrew Phillips
  
  Bioinformatics | January 2014, Vol 30: pp. 1491-1492
  
  Publication Publication
- Compiling DNA Strand Displacement Reactions Using a Functional Programming Language
  
  Matthew R Lakin, Andrew Phillips
  
  Practical Aspects of Declarative Languages - 16th International Symposium | January 2014
  
  Publication Project
- Programmable chemical controllers made from DNA
  
  Yuan-Jyue Chen, Neil Dalchau, Niranjan Srnivas, Andrew Phillips, Luca Cardelli, David Soloveichik, Georg Seelig
  
  Nature Nanotechnology | September 2013, Vol 8: pp. 755-762
  
  Publication Project
- The circadian clock has transient plasticity of period and is required for timing of nocturnal processes in Arabidopsis
  
  Antony N Dodd, Neil Dalchau, Michael J Gardner, Seong Jin Baek, Alex AR Webb
  
  New Phytologist | September 2013, Vol 201(1): pp. 168-179
  
  Publication
- Functional Analysis of Large-scale DNA Strand Displacement Circuits
  
  Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, Andrew Phillips, Hillel Kugler
  
  International Conference on DNA Computing and Molecular Programming | September 2013
  
  Publication Publication Project Project
- Modular verification of DNA strand displacement networks via serializability analysis
  
  Matthew R. Lakin, Andrew Phillips, Darko Stefanovic
  
  International Conference on DNA Computing and Molecular Programming | September 2013, Vol 8141: pp. 133-146
  
  Publication Publication Publication Project
- Automated Ratiometric Characterization using GEC
  
  Paul Grant, Jim Haseloff, Stephen Emmott, Boyan Yordanov, Neil Dalchau, Andrew Phillips
  
  International Workshop on Biodesign Automation | July 2013
  
  Publication Project
- Design and Analysis of DNA Strand Displacement Devices using Probabilistic Model Checking
  
  Matthew R. Lakin,, David Parker, Luca Cardelli, Marta Kwiatkowska, Andrew Phillips
  
  Journal of the Royal Society Interface | July 2012, Vol 9: pp. 1470-1485
  
  Publication Project
- Computational Modeling of Synthetic Microbial Biofilms
  
  Timothy J. Rudge, Paul J. Steiner, Andrew Phillips, Jim Haseloff
  
  ACS Synthetic Biology | July 2012, Vol 1: pp. 345-352
  
  Publication Project
- Stochastic Simulation of Multiple Process Calculi for Biology
  
  Matthew R. Lakin, Loïc Paulevé, Andrew Phillips
  
  Theoretical Computer Science | May 2012, Vol 431: pp. 181-206
  
  Publication Publication Project Project
- Towards the rational design of synthetic cells with prescribed population dynamics
  
  Neil Dalchau, Matthew Smith, Samuel Martin, James R Brown, Stephen Emmott, Andrew Phillips
  
  Journal of the Royal Society Interface | May 2012, Vol 9: pp. 2883-2898
  
  Publication Project
- Abstractions for DNA circuit design
  
  Matthew R Lakin, Simon Youssef, Luca Cardelli, Andrew Phillips
  
  Journal of the Royal Society Interface | March 2012, Vol 9(68): pp. 470-486
  
  Publication Publication Project
- Understanding biological timing using mechanistic and black-box models
  
  Neil Dalchau
  
  New Phytologist | March 2012, Vol 193(4): pp. 852-858
  
  Publication
- A model of stem cell population dynamics: in-silico analysis and in-vivo validation
  
  Hillel Kugler
  
  Development | January 2012, Vol 139: pp. 47
  
  Publication Publication Publication
- Visual DSD: a design and analysis tool for DNA strand displacement systems
  
  Matthew R Lakin, Simon Youssef, Filippo Polo, Stephen Emmott, Andrew Phillips
  
  Bioinformatics | November 2011, Vol 27: pp. 3211-3213
  
  Publication Project
- A peptide filtering relation quantifies MHC class I peptide optimization
  
  Neil Dalchau, Andrew Phillips, Leonard D Goldstein, Mark Howarth, Luca Cardelli, Stephen Emmott, Tim Elliott, Joern M Werner
  
  PLoS Computational Biology | October 2011, Vol 7(10): pp. e1002144
  
  Publication Publication Project Project
- Modelling, simulating and verifying Turing-powerful strand displacement systems
  
  Andrew Phillips, Matthew R Lakin
  
  International Conference on DNA Computing and Molecular Programming | September 2011
  
  Publication DOI Project
- Localized Hybridization Circuits
  
  Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif
  
  International Conference on DNA Computing and Molecular Programming | September 2011, Vol 6937: pp. 64-83
  
  Publication Publication Publication Project
- The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose
  
  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, Alex AR Webb
  
  Proceedings of the National Academy of Sciences | March 2011
  
  Publication
- Ticking Over – Circadian Systems Across the Kingdoms of Life
  
  Neil Dalchau, Alex AR Webb
  
  Biochemist | February 2011, Vol 33(1): pp. 12-15
  
  Publication
- Correct biological timing in Arabidopsis requires multiple light signaling pathways
  
  Neil Dalchau, Katharine E Hubbard, Fiona C Robertson, Carlos T Hotta, Helen M Briggs, Guy-Bart Stan, Jorge M Goncalves, Alex A R Webb
  
  Proceedings of the National Academy of Sciences | July 2010
  
  Publication
- Disruption of two defensive signaling pathways by a viral RNA silencing suppressor
  
  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, John P Carr
  
  Molecular Plant-Microbe Interations | January 2010, Vol 23: pp. 835-845
  
  Publication
- A Process Model of Rho GTP-binding Proteins
  
  Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanogullari, Andrew Phillips
  
  Theoretical Computer Science | August 2009, Vol 410: pp. 3166-3185
  
  Publication Publication Project
- Systems analyses of circadian networks
  
  Katharine E. Hubbard, Fiona C. Robertson, Neil Dalchau, Alex A. R. Webb
  
  Molecular Biosystems | August 2009, Vol 5: pp. 1502-1511
  
  Publication Publication
- Towards programming languages for genetic engineering of living cells
  
  Michael Pedersen, Andrew Phillips
  
  Journal of the Royal Society Interface | April 2009, Vol 6: pp. S437-S450
  
  Publication Publication Publication Project
- A Process Model of Actin Polymerisation
  
  Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanoğulları, Andrew Phillips
  
  Electronic Notes in Theoretical Computer Science | February 2009, Vol 229(1): pp. 127-144
  
  Publication Publication Project
- An Abstract Machine for the Stochastic Bioambient Calculus
  
  Andrew Phillips
  
  Electronic Notes in Theoretical Computer Science | January 2009, Vol 227: pp. 143-159
  
  Publication Publication Project
- A Visual Process Calculus for Biology
  
  Andrew Phillips
  
  Symbolic Systems Biology: Theory and Methods | Published by Jones and Bartlett Publishers | 2009 | Symbolic Systems Biology: Theory and Methods edition
  
  Publication Project
- Fast enumeration of non-isomorphic chemical reaction networks
  
  Carlo Spaccasassi, Boyan Yordanov, Andrew Phillips, Neil Dalchau
  
  Computational Methods for Systems Biology (CMSB) | September 2019
  
  Editor(s): Luca Bortolussi, Guido Sanguinetti
  
  Author's Version Publication
- A Generic Abstract Machine for Stochastic Process Calculi
  
  Loïc Paulevé, Simon Youssef, Matthew R. Lakin, Andrew Phillips
  
  Computational Methods in Systems Biology | September 2010, pp. 43-54
  
  Publication Publication Project
- Computing with biological switches and clocks
  
  Neil Dalchau, Gregory Szep, Rosa Hernansaiz-Ballesteros, Chris P Barnes, Luca Cardelli, Andrew Phillips, Attila Csikasz-Nagy
  
  Natural Computing | June 2018
  
  Publication Publication Project Project

- A deep learning model for predicting next-generation sequencing depth from DNA sequence
  
  Jinny X. Zhang, Boyan Yordanov, Alexander Gaunt, Michael X. Wang, Peng Dai, Yuan-Jyue Chen, Kerou Zhang, John Z. Fang, Neil Dalchau, Jiaming Li, Andrew Phillips, David Yu Zhang
  
  Nature Communications | July 2021, Vol 12
  
  Publication Project
- A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction.
  
  Trevor Y. H. Ho, Alexander Shao, Zeyu Lu, Harri Savilahti, Filippo Menolascina, Lei Wang, Neil Dalchau, Baojun Wang
  
  Nature Communications | April 2021, Vol 12(1): pp. 2200-2200
  
  DOI Publication
- Interpretation of morphogen gradients by a synthetic bistable circuit
  
  Paul Grant, Gregory Szep, Om Patange, Jacob Halatek, Valerie Coppard, Attila Csikasz-Nagy, Jim Haseloff, James C. W. Locke, Neil Dalchau, Andrew Phillips
  
  Nature Communications | November 2020, Vol 11(5545)
  
  Publication Project
- Turing Patterning in Stratified Domains
  
  Andrew L. Krause, Vaclav Klika, Jacob Halatek, Paul Grant, Thomas L. Woolley, Neil Dalchau, Eamonn A. Gaffney
  
  Bulletin of Mathematical Biology | October 2020, Vol 82(136)
  
  Publication Publication Project
- Domain-specific programming languages for computational nucleic acid systems
  
  Matthew R. Lakin, Andrew Phillips
  
  ACS Synthetic Biology | June 2020, Vol 9(7): pp. 1499-1513
  
  Publication Project
- Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms
  
  Eugene Nadezhdin, Niall Murphy, Neil Dalchau, Andrew Phillips, James C. W. Locke
  
  Nature Communications | February 2020, Vol 11: pp. 950
  
  Publication Project
- DNA-based communication in populations of synthetic protocells
  
  Alex Joesaar, Shuo Yang, Bas Bögels, Ardjan van der Linden, Pascal Pieters, B. V. V. S. Pavan Kumar, Neil Dalchau, Andrew Phillips, Stephen Mann, Tom F. A. de Greef
  
  Nature Nanotechnology | March 2019
  
  Publication DOI Project
- A common molecular logic determines embryonic stem cell self-renewal and reprogramming
  
  Sara-Jane Dunn, Meng Amy Li, Elena Carbognin, Austin Smith, Graziano Martello
  
  The EMBO Journal | November 2018, Vol e100003
  
  DOI Publication Project
- A Logic Programming Language for Computational Nucleic Acid Devices
  
  Carlo Spaccasassi, Matthew R. Lakin, Andrew Phillips
  
  ACS Synthetic Biology | October 2018
  
  Publication Project
- Escherichia coli can survive stress by noisy growth modulation
  
  Om Patange, Christian Schwall, Matt Jones, Casandra Villava, Douglas A. Griffith, Andrew Phillips, James C.W. Locke
  
  Nature Communications | September 2018, Vol 53(33)
  
  Publication Project
- Synthesizing and tuning stochastic chemical reaction networks with specified behaviours
  
  Niall Murphy, Rasmus Petersen, Andrew Phillips, Boyan Yordanov, Neil Dalchau
  
  Journal of the Royal Society Interface | August 2018
  
  Publication Publication Project Project
- A Mechanistic Model for Predicting Cell Surface Presentation of Competing Peptides by MHC Class I Molecules
  
  Denise S. M. Boulanger, Ruth C. Eccleston, Andrew Phillips, Peter V. Coveney, T. Elliott, Neil Dalchau
  
  Frontiers in Immunology | July 2018, Vol 9: pp. 1538
  
  Publication Publication Project
- Computing with biological switches and clocks
  
  Neil Dalchau, Gregory Szep, Rosa Hernansaiz-Ballesteros, Chris P Barnes, Luca Cardelli, Andrew Phillips, Attila Csikasz-Nagy
  
  Natural Computing | June 2018
  
  Publication Publication Project Project
- Model reduction enables Turing instability analysis of large reaction–diffusion models
  
  Stephen Smith, Neil Dalchau
  
  Journal of the Royal Society Interface | March 2018, Vol 15
  
  Publication Publication Project
- Predicting DNA hybridization kinetics from sequence
  
  Jinny X. Zhang, John Z. Fang, Wei Duan, Lucia R. Wu, Angela W. Zhang, Neil Dalchau, Boyan Yordanov, Rasmus Petersen, Andrew Phillips, David Yu Zhang
  
  Nature Chemistry | November 2017
  
  Publication Publication Project Project
- Host genotype and time dependent antigen presentation of viral peptides: predictions from theory
  
  Ruth Charlotte Eccleston, Peter V. Coveney, Neil Dalchau
  
  Scientific Reports | October 2017, Vol 7: pp. 14367
  
  Publication Publication Project
- A protein phosphatase network controls the temporal and spatial dynamics of differentiation commitment in human epidermis
  
  Ajay Mishra, Benedicte Oules, Angela Oliveira Pisco, Tony Ly, Kifayathullah Liakath-Ali, Gernot Walko, Priyalakshmi Viswanathan, Matthieu Tihy, Jagdeesh Nijjher, Sara-Jane Dunn, Angus I Lamond, Fiona M Watt
  
  eLife | October 2017, Vol 6:e27356
  
  Publication DOI
- A spatially localized architecture for fast and modular DNA computing
  
  Gourab Chatterjee, Neil Dalchau, Richard A. Muscat, Andrew Phillips, Georg Seelig
  
  Nature Nanotechnology | July 2017
  
  Publication Publication Project
- The Role of Multiscale Protein Dynamics in Antigen Presentation and T Lymphocyte Recognition
  
  Ruth Charlotte Eccleston, Shunzhou Wan, Neil Dalchau, Peter V. Coveney
  
  Frontiers in Immunology | July 2017
  
  Publication DOI PDF Project
- Efficient Switches in Biology and Computer Science
  
  Luca Cardelli, Rosa D Hernansaiz-Ballesteros, Neil Dalchau, Attila Csikasz-Nagy
  
  PLoS Computational Biology | January 2017, Vol 13: pp. e1005100
  
  Publication Publication Publication
- How computational models contribute to our understanding of the germ line
  
  Kathryn Atwell, Sara-Jane Dunn, James M. Osborne, Hillel Kugler, E. Jane Albert Hubbard
  
  Molecular Reproduction and Development | September 2016
  
  Publication Publication
- A Method to Identify and Analyze Biological Programs through Automated Reasoning
  
  Boyan Yordanov, Sara-Jane Dunn, Hillel Kugler, Austin Smith, Graziano Martello, Stephen Emmott
  
  Systems Biology and Applications | July 2016, Vol 2
  
  Publication Publication
- A strand graph semantics for DNA-based computation
  
  Rasmus Petersen, Matthew R Lakin, Andrew Phillips
  
  Theoretical Computer Science | June 2016, Vol 632: pp. 43-73
  
  Publication Publication Project
- Modular verification of chemical reaction network encodings via serializability analysis
  
  Matthew R Lakin, Darko Stefanovic, Andrew Phillips
  
  Theoretical Computer Science | June 2016, Vol 632: pp. 21
  
  Publication Project
- Automated Synthesis and Analysis of Switching Gene Regulatory Networks
  
  Yoli Shavit, Boyan Yordanov, Sara-Jane Dunn, Christoph M. Wintersteiger, Tomoki Otani, Frederick J. Livesey, Hillel Kugler
  
  Biosystems | May 2016, Vol 146: pp. 26-34
  
  Publication Publication Publication
- Combined Changes in Wnt Signalling Response and Contact Inhibition Induce Altered Proliferation in Radiation Treated Intestinal Crypts
  
  Sara-Jane Dunn, James M. Osborne, Inke S. Nathke
  
  Molecular Biology of the Cell | April 2016, Vol 27: pp. 1863-1874
  
  Publication Publication
- Noise Reduction in Complex Biological Switches
  
  Attila Csikasz-Nagy, Neil Dalchau, Mirco Tribastone, Max Tschaikowski, Luca Cardelli
  
  Scientific Reports | February 2016, Vol 6: pp. 20214
  
  Publication Publication
- Selector function of MHC I molecules is determined by protein plasticity
  
  Alistair Bailey, Neil Dalchau, Rachel Carter, Stephen Emmott, Andrew Phillips, Jörn M. Werner, Tim Elliott
  
  Scientific Reports | October 2015, Vol 5: pp. 14928
  
  Publication Publication Project
- Characterization of intrinsic properties of promoters
  
  Timothy J. Rudge, James R. Brown, Fernan Federici, Neil Dalchau, Andrew Phillips, James W Ajioka, Jim Haseloff
  
  ACS Synthetic Biology | October 2015
  
  Publication Publication Project
- Synthesizing and tuning chemical reaction networks with specified behaviours
  
  Neil Dalchau, Niall Murphy, Rasmus Petersen, Boyan Yordanov
  
  International Conference on DNA Computing and Molecular Programming | August 2015, Vol 9211
  
  Publication Publication Publication Project
- Probabilistic analysis of localized DNA hybridization circuits
  
  Neil Dalchau, Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif
  
  ACS Synthetic Biology | June 2015, Vol 4: pp. 898-913
  
  Publication Publication Project
- A High-Level Language for Rule-Based Modelling
  
  Michael Pedersen, Andrew Phillips, Gordon D. Plotkin
  
  PLoS ONE | June 2015, Vol 10(6): pp. e0114296
  
  Publication
- Is ‘peak N’ key to understanding the timing of flowering in annual plants?
  
  Camille Guilbaud, Neil Dalchau, Drew Purves, Lindsay Turnbull
  
  New Phytologist | January 2015, Vol 205: pp. 918-927
  
  Publication
- Computational design of nucleic acid feedback control circuits
  
  Boyan Yordanov, Jongmin Kim, Rasmus L. Petersen, Angelina Shudy, Vishwesh V. Kulkarni, Andrew Phillips
  
  ACS Synthetic Biology | July 2014, Vol 3: pp. 600-616
  
  Publication Publication Project
- Defining an essential transcriptional factor program for naive pluripotency
  
  Sara-Jane Dunn, Graziano Martello, Boyan Yordanov, Stephen Emmott, Austin Smith
  
  Science | June 2014, Vol 344: pp. 1156
  
  Publication Project
- A Computational Method for Automated Characterization of Genetic Components
  
  Neil Dalchau, Boyan Yordanov, Paul Grant, Michael Pedersen, Stephen Emmott, Jim Haseloff, Andrew Phillips
  
  ACS Synthetic Biology | March 2014, Vol 3(8): pp. 578-588
  
  Publication Publication Project
- Ten Simple Rules for Effective Computational Research
  
  James Osborne, Miguel Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander Fletcher, Derek Groen, Bernhard Knapp, Gary Mirams, Joe Pitt-Francis, Biswa Sengupta, David Wright, Christian Yates, David Gavaghan, Stephen Emmott, Charlotte Deane
  
  PLoS Computational Biology | March 2014, pp. e1003506
  
  Publication
- Bio Simulators: a web UI for biological simulation
  
  Michael Pedersen, Nicolas Oury, Andrew Phillips
  
  Bioinformatics | January 2014, Vol 30: pp. 1491-1492
  
  Publication Publication
- Programmable chemical controllers made from DNA
  
  Yuan-Jyue Chen, Neil Dalchau, Niranjan Srnivas, Andrew Phillips, Luca Cardelli, David Soloveichik, Georg Seelig
  
  Nature Nanotechnology | September 2013, Vol 8: pp. 755-762
  
  Publication Project
- The circadian clock has transient plasticity of period and is required for timing of nocturnal processes in Arabidopsis
  
  Antony N Dodd, Neil Dalchau, Michael J Gardner, Seong Jin Baek, Alex AR Webb
  
  New Phytologist | September 2013, Vol 201(1): pp. 168-179
  
  Publication
- Modular verification of DNA strand displacement networks via serializability analysis
  
  Matthew R. Lakin, Andrew Phillips, Darko Stefanovic
  
  International Conference on DNA Computing and Molecular Programming | September 2013, Vol 8141: pp. 133-146
  
  Publication Publication Publication Project
- Chaste: An Open Source C++ Library for Computational Physiology and Biology
  
  G. R. Mirams, C. J. Arthurs, M. O. Bernabeu, R. Bordas, J. Cooper, A. Corrias, Y. Davit, Sara-Jane Dunn, A. G. Fletcher, D. G. Harvey, M. E. Marsh, J. M. Osborne, P. Pathmanathan, J. Pitt-Francis, J. Southern, N. Zemzemi, D. J. Gavaghan
  
  PLOS Comput. Biol. | March 2013
  
  Publication
- Oligodendrocyte dynamics in the healthy adult CNS: evidence for myelin remodelling
  
  Kaylene M. Young, Konstantina Psachoulia, Richa B. Tripathi, Sara-Jane Dunn, Lee Cossell, David Attwell, Koujiro Tohyama, William D. Richardson
  
  Neuron | March 2013
  
  Publication
- Design and Analysis of DNA Strand Displacement Devices using Probabilistic Model Checking
  
  Matthew R. Lakin,, David Parker, Luca Cardelli, Marta Kwiatkowska, Andrew Phillips
  
  Journal of the Royal Society Interface | July 2012, Vol 9: pp. 1470-1485
  
  Publication Project
- Computational Modeling of Synthetic Microbial Biofilms
  
  Timothy J. Rudge, Paul J. Steiner, Andrew Phillips, Jim Haseloff
  
  ACS Synthetic Biology | July 2012, Vol 1: pp. 345-352
  
  Publication Project
- A Two-Dimensional Model of the Colonic Crypt Accounting for the Role of the Basement Membrane and Pericryptal Fibroblast Sheath
  
  Sara-Jane Dunn, Paul L. Appleton, Scott A. Nelson, Inke S. Nathke, David J. Gavaghan, James M. Osborne
  
  PLoS Computational Biology | May 2012
  
  Publication
- Stochastic Simulation of Multiple Process Calculi for Biology
  
  Matthew R. Lakin, Loïc Paulevé, Andrew Phillips
  
  Theoretical Computer Science | May 2012, Vol 431: pp. 181-206
  
  Publication Publication Project Project
- Towards the rational design of synthetic cells with prescribed population dynamics
  
  Neil Dalchau, Matthew Smith, Samuel Martin, James R Brown, Stephen Emmott, Andrew Phillips
  
  Journal of the Royal Society Interface | May 2012, Vol 9: pp. 2883-2898
  
  Publication Project
- Abstractions for DNA circuit design
  
  Matthew R Lakin, Simon Youssef, Luca Cardelli, Andrew Phillips
  
  Journal of the Royal Society Interface | March 2012, Vol 9(68): pp. 470-486
  
  Publication Publication Project
- Understanding biological timing using mechanistic and black-box models
  
  Neil Dalchau
  
  New Phytologist | March 2012, Vol 193(4): pp. 852-858
  
  Publication
- A model of stem cell population dynamics: in-silico analysis and in-vivo validation
  
  Hillel Kugler
  
  Development | January 2012, Vol 139: pp. 47
  
  Publication Publication Publication
- Modelling the role of the basement membrane beneath a growing epithelial monolayer
  
  Sara-Jane Dunn, Alexander G. Fletcher, S. Jonathan Chapman, David J. Gavaghan, James M. Osborne
  
  Journal of Theoretical Biology | December 2011
  
  Publication
- Visual DSD: a design and analysis tool for DNA strand displacement systems
  
  Matthew R Lakin, Simon Youssef, Filippo Polo, Stephen Emmott, Andrew Phillips
  
  Bioinformatics | November 2011, Vol 27: pp. 3211-3213
  
  Publication Project
- A peptide filtering relation quantifies MHC class I peptide optimization
  
  Neil Dalchau, Andrew Phillips, Leonard D Goldstein, Mark Howarth, Luca Cardelli, Stephen Emmott, Tim Elliott, Joern M Werner
  
  PLoS Computational Biology | October 2011, Vol 7(10): pp. e1002144
  
  Publication Publication Project Project
- How neurons migrate: a dynamic in-silico model of neuronal migration in the developing cortex
  
  Yaki Setty, Chih-Chun Chen, Maria Secrier, Nikita Skoblov, Dimitrios Kalamatianos, Stephen Emmott
  
  BMC Systems Biology | September 2011
  
  Publication
- Localized Hybridization Circuits
  
  Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif
  
  International Conference on DNA Computing and Molecular Programming | September 2011, Vol 6937: pp. 64-83
  
  Publication Publication Publication Project
- Ticking Over – Circadian Systems Across the Kingdoms of Life
  
  Neil Dalchau, Alex AR Webb
  
  Biochemist | February 2011, Vol 33(1): pp. 12-15
  
  Publication
- The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding
  
  Andy van Hateren, Ed James, Alistair Bailey, Andrew Phillips, Neil Dalchau, Tim Elliott
  
  Tissue Antigens | October 2010, Vol 76(4): pp. 259
  
  Publication Publication Project
- A Generic Abstract Machine for Stochastic Process Calculi
  
  Loïc Paulevé, Simon Youssef, Matthew R. Lakin, Andrew Phillips
  
  Computational Methods in Systems Biology | September 2010, pp. 43-54
  
  Publication Publication Project
- Modeling Alveolar Volume Changes During Periodic Breathing in Heterogeneously Ventilated Lungs
  
  Sara-Jane Dunn, Jonathan P. Whiteley
  
  Annals of Biomedical Engineering | September 2010, Vol 38: pp. 2988-2999
  
  Publication Publication
- Biocharts: A Visual Formalism for Complex Biological Systems
  
  Hillel Kugler, Antti Larjo, David Harel
  
  Journal of the Royal Society Interface | July 2010, Vol 7: pp. 1015-1024
  
  Published online December 2009
  
  Publication Publication
- The Neuroepithelial Basement Membrane Serves As A Boundary And A Substrate For Neuron Migration In The Zebrafish Hindbrain
  
  Paul Grant, Cecilia Moens
  
  Neural Development | March 2010, Vol 5
  
  Publication Publication Publication
- Disruption of two defensive signaling pathways by a viral RNA silencing suppressor
  
  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, John P Carr
  
  Molecular Plant-Microbe Interations | January 2010, Vol 23: pp. 835-845
  
  Publication
- Computational Modeling of the EGFR Network Elucidates Control Mechanisms Regulating Signal Dynamics
  
  Dennis YQ Wang, Luca Cardelli, Andrew Phillips, Nir Piterman, Jasmin Fisher
  
  BMC Systems Biology | December 2009, Vol 3: pp. 118
  
  Publication Project
- A Process Model of Rho GTP-binding Proteins
  
  Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanogullari, Andrew Phillips
  
  Theoretical Computer Science | August 2009, Vol 410: pp. 3166-3185
  
  Publication Publication Project
- Systems analyses of circadian networks
  
  Katharine E. Hubbard, Fiona C. Robertson, Neil Dalchau, Alex A. R. Webb
  
  Molecular Biosystems | August 2009, Vol 5: pp. 1502-1511
  
  Publication Publication
- A programming language for composable DNA circuits
  
  Andrew Phillips, Luca Cardelli
  
  Journal of the Royal Society Interface | June 2009, Vol 6: pp. S419-S436
  
  Publication Publication Project
- Towards programming languages for genetic engineering of living cells
  
  Michael Pedersen, Andrew Phillips
  
  Journal of the Royal Society Interface | April 2009, Vol 6: pp. S437-S450
  
  Publication Publication Publication Project
- A Process Model of Actin Polymerisation
  
  Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanoğulları, Andrew Phillips
  
  Electronic Notes in Theoretical Computer Science | February 2009, Vol 229(1): pp. 127-144
  
  Publication Publication Project
- An Abstract Machine for the Stochastic Bioambient Calculus
  
  Andrew Phillips
  
  Electronic Notes in Theoretical Computer Science | January 2009, Vol 227: pp. 143-159
  
  Publication Publication Project
- Fast enumeration of non-isomorphic chemical reaction networks
  
  Carlo Spaccasassi, Boyan Yordanov, Andrew Phillips, Neil Dalchau
  
  Computational Methods for Systems Biology (CMSB) | September 2019
  
  Editor(s): Luca Bortolussi, Guido Sanguinetti
  
  Author's Version Publication
- Efficient Amortised Bayesian Inference for Hierarchical and Nonlinear Dynamical Systems
  
  Geoffrey Roeder, Paul Grant, Andrew Phillips, Neil Dalchau, Ted Meeds
  
  ICML 2019 | June 2019
  
  Author's Version PDF Project Project
- Formal Analysis of Network Motifs
  
  Hillel Kugler, Sara-Jane Dunn, Boyan Yordanov
  
  CMSB | September 2018
  
  Publication DOI Project
- Automated, Constraint-Based Analysis of Tethered DNA Nanostructures
  
  Matthew R. Lakin, Andrew Phillips
  
  International Conference on DNA Computing and Molecular Programming | September 2017
  
  Publication Publication Project
- Algebraic Polynomial-based Synthesis for Abstract Boolean Network Analysis
  
  Peter Backeman, Sara-Jane Dunn, Boyan Yordanov, Christoph M. Wintersteiger, Sara-Jane Dunn, Boyan Yordanov, Christoph M. Wintersteiger
  
  Proceedings of the 14th International Workshop on Satisfiability Modulo Theories (SMT) | July 2016
  
  Publication Project
- Computational algorithms as biological switches
  
  Rosa Hernansaiz-Ballesteros, Neil Dalchau, Luca Cardelli, Attila Csikasz-Nagy
  
  Proceedings of the Evry Spring School on Advances in Systems and Synthetic Biology | March 2016
  
  Publication Project
- Computational design of reaction-diffusion patterns using DNA-based chemical reaction networks
  
  Neil Dalchau, Georg Seelig, Andrew Phillips
  
  International Conference on DNA Computing and Molecular Programming | September 2014
  
  Publication Publication Publication Project
- Abstract modelling of tethered DNA circuits
  
  Matthew R. Lakin, Rasmus Petersen, Kathryn E. Gray, Andrew Phillips
  
  International Conference on DNA Computing and Molecular Programming | September 2014
  
  Publication Publication Publication Project
- Analyzing and Synthesizing Genomic Logic Functions
  
  Nicola Paoletti, Boyan Yordanov, Youssef Hamadi, Christoph M. Wintersteiger, Hillel Kugler
  
  26th International Conference on Computer Aided Verification (CAV) | July 2014
  
  Publication Publication Publication Project
- Compiling DNA Strand Displacement Reactions Using a Functional Programming Language
  
  Matthew R Lakin, Andrew Phillips
  
  Practical Aspects of Declarative Languages - 16th International Symposium | January 2014
  
  Publication Project
- Biocharts: Unifying Biological Hypotheses with Models and Experiments
  
  Hillel Kugler
  
  IEEE 9th International Conference on e-Science | October 2013
  
  Publication
- Functional Analysis of Large-scale DNA Strand Displacement Circuits
  
  Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, Andrew Phillips, Hillel Kugler
  
  International Conference on DNA Computing and Molecular Programming | September 2013
  
  Publication Publication Project Project
- Automated Ratiometric Characterization using GEC
  
  Paul Grant, Jim Haseloff, Stephen Emmott, Boyan Yordanov, Neil Dalchau, Andrew Phillips
  
  International Workshop on Biodesign Automation | July 2013
  
  Publication Project
- Z34Bio: An SMT-based Framework for Analyzing Biological Computation
  
  Boyan Yordanov, Youssef Hamadi, Hillel Kugler, Christoph M. Wintersteiger
  
  SMT'13 | July 2013
  
  Publication Project
- SMT-based Analysis of Biological Computation
  
  Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, Hillel Kugler
  
  NASA Formal Methods Symposium 2013 | May 2013
  
  Publication Project
- Modelling, simulating and verifying Turing-powerful strand displacement systems
  
  Andrew Phillips, Matthew R Lakin
  
  International Conference on DNA Computing and Molecular Programming | September 2011
  
  Publication DOI Project
- Synthesizing Biological Theories
  
  Hillel Kugler, Cory Plock, Andy Roberts
  
  Computer Aided Verification (CAV'11) | July 2011
  
  Publication Download
- Model Checking Using SMT and Theory of Lists
  
  Aleksandar Milicevic, Hillel Kugler
  
  Nasa Formal Methods Symposium | April 2011
  
  Nasa Formal Methods Symposium
  
  Publication Publication
- The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose
  
  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, Alex AR Webb
  
  Proceedings of the National Academy of Sciences | March 2011
  
  Publication
- Stochastic Simulation of Process Calculi for Biology
  
  Andrew Phillips, Matthew R. Lakin, Loïc Paulevé
  
  Electronic Proceedings in Theoretical Computer Science | November 2010
  
  Publication Publication Project
- Correct biological timing in Arabidopsis requires multiple light signaling pathways
  
  Neil Dalchau, Katharine E Hubbard, Fiona C Robertson, Carlos T Hotta, Helen M Briggs, Guy-Bart Stan, Jorge M Goncalves, Alex A R Webb
  
  Proceedings of the National Academy of Sciences | July 2010
  
  Publication
- Accelerating Smart Play-Out
  
  David Harel, Hillel Kugler, Shahar Maoz, Itai Segali
  
  SOFSEM 2010: Theory and Practice of Computer Science | January 2010
  
  Publication Publication
- Some Thoughts on the Semantics of Biocharts
  
  David Harel, Hillel Kugler
  
  Essays in Memory of Amir Pnueli | January 2010
  
  Dedicated to the dear memory of Amir Pnueli: Friend, mentor, colleague, and a truly towering figure in computer science
  
  Publication Publication
- Controller Synthesis from LSC Requirements
  
  Hillel Kugler, Cory Plock, Amir Pnueli
  
  Fundamental Approaches to Software Engineering (FASE'09) | March 2009
  
  Publication Publication
- Compositional Synthesis of Reactive Systems from Live Sequence Chart Specifications
  
  Hillel Kugler
  
  Tools and Algorithms for the Construction and Analysis of Systems (TACAS'09) | March 2009
  
  Publication Publication
- How Hard is Smart Play-Out? On the Complexity of Verification-Driven Execution
  
  David Harel, Hillel Kugler, Shahar Maoz, Itai Segall
  
  Perspectives in Concurrency Theory (Festschrift for P.S. Thiagarajan), (K. Lodaya et al, eds.), University Press (India) | January 2009
  
  Perspectives in Concurrency Theory (Festschrift for P.S. Thiagarajan), (K. Lodaya et al, eds.), University Press (India)
  
  Publication
- What makes a biological clock efficient?
  
  Attila Csikász-Nagy, Neil Dalchau
  
  MSR-TR-2014-134 | September 2014
  
  Essays for the Luca Cardelli Fest
  
  Publication
- Z3-4Biology SMT-Based Analysis of Biological Computation
  
  Boyan Yordanov, Youssef Hamadi, Hillel Kugler, Christoph M. Wintersteiger
  
  MSR-TR-2012-31 | March 2012
  
  Publication Project
- Understanding and predicting biological networks using linear system identification
  
  Alberto Carignano, Ye Yuan, Neil Dalchau, Alex AR Webb, Jorge M Goncalves
  
  A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations, 9 | Published by Springer | 2014 | A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations edition
  
  Publication Publication
- A Visual Process Calculus for Biology
  
  Andrew Phillips
  
  Symbolic Systems Biology: Theory and Methods | Published by Jones and Bartlett Publishers | 2009 | Symbolic Systems Biology: Theory and Methods edition
  
  Publication Project