Publications

Automated Leak Analysis of Nucleic Acid Circuits

Iuliia Zarubiieva, Carlo Spaccasassi, Vishwesh Kulkarni, Andrew Phillips.
ACS Synthetic Biology (2022)
PDF Project
Automated Leak Analysis of Nucleic Acid Circuits

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 (2021)
PDF Project
A deep learning model for predicting next-generation sequencing depth from DNA sequence

Interpretation of morphogen gradients by a synthetic bistable circuit

Paul K Grant, Gregory Szep, Om Patange, Jacob Halatek, Valerie Coppard, Attila Csikász-Nagy, Jim Haseloff, James CW Locke, Neil Dalchau, Andrew Phillips.
Nature Communications (2020)
PDF Project
Interpretation of morphogen gradients by a synthetic bistable circuit

Domain-Specific Programming Languages for Computational Nucleic Acid Systems

Matthew R Lakin, Andrew Phillips.
ACS Synthetic Biology (2020)
PDF 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 CW Locke.
Nature Communications (2020)
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Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms

Fast Enumeration of Non-isomorphic Chemical Reaction Networks

Carlo Spaccasassi, Boyan Yordanov, Andrew Phillips, Neil Dalchau.
Computational Methods in Systems Biology (CMSB) (2019)
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A Logic Programming Language for Computational Nucleic Acid Devices

Carlo Spaccasassi, Matthew R Lakin, Andrew Phillips.
ACS Synthetic Biology (2019)
PDF Project
A Logic Programming Language for Computational Nucleic Acid Devices

Efficient Amortised Bayesian Inference for Hierarchical and Nonlinear Dynamical Systems

Geoffrey Roeder, Paul K. Grant, Andrew Phillips, Neil Dalchau, Edward Meeds.
International Conference on Machine Learning (ICML) (2019)
PDF Project

DNA-based communication in populations of synthetic protocells

Alex Joesaar, Shuo Yang, Bas Bögels, Ardjan van der Linden, Pascal Pieters, BVVS Pavan Kumar, Neil Dalchau, Andrew Phillips, Stephen Mann, Tom FA de Greef.
Nature Nanotechnology (2019)
PDF Project
DNA-based communication in populations of synthetic protocells

Escherichia coli can survive stress by noisy growth modulation

Om Patange, Christian Schwall, Matt Jones, Casandra Villava, Douglas A Griffith, Andrew Phillips, James CW Locke.
Nature Communications (2018)
PDF Project
Escherichia coli can survive stress by noisy growth modulation

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 (2018)
PDF Project
Predicting DNA hybridization kinetics from sequence

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 (2018)
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A Mechanistic Model for Predicting Cell Surface Presentation of Competing Peptides by MHC Class I Molecules

Denise SM Boulanger, Ruth Charlotte Eccleston, Andrew Phillips, Peter V Coveney, Tim Elliott, Neil Dalchau.
Frontiers in Immunology (2018)
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Automated analysis of tethered DNA nanostructures using constraint solving

Matthew R Lakin, Andrew Phillips.
Natural Computing (2018)
PDF Project

Computing with biological switches and clocks

Neil Dalchau, Gregory Szép, Rosa Hernansaiz-Ballesteros, Chris P Barnes, Luca Cardelli, Andrew Phillips, Attila Csikász-Nagy.
Natural Computing (2018)
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Automated, Constraint-Based Analysis of Tethered DNA Nanostructures

Matthew R Lakin, Andrew Phillips.
DNA Computing and Molecular Programming (DNA) (2017)
PDF Project

A spatially localized architecture for fast and modular DNA computing

Gourab Chatterjee, Neil Dalchau, Richard A Muscat, Andrew Phillips, Georg Seelig.
Nature Nanotechnology (2017)
PDF Project
A spatially localized architecture for fast and modular DNA computing

Modular verification of chemical reaction network encodings via serializability analysis

Matthew R Lakin, Darko Stefanovic, Andrew Phillips.
Theoretical Computer Science (2016)
PDF Project

A strand graph semantics for DNA-based computation

Rasmus L Petersen, Matthew R Lakin, Andrew Phillips.
Theoretical Computer Science (2016)
PDF 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 (2016)
PDF Project

Orthogonal intercellular signaling for programmed spatial behavior.

Paul K Grant, Neil Dalchau, James R Brown, Fernan Federici, Timothy J Rudge, Boyan Yordanov, Om Patange, Andrew Phillips, Jim Haseloff.
Molecular Systems Biology (2016)
PDF Project
Orthogonal intercellular signaling for programmed spatial behavior.

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 (2015)
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Probabilistic Analysis of Localized DNA Hybridization Circuits

Neil Dalchau, Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif.
ACS Synthetic Biology (2015)
PDF Project

A High-Level Language for Rule-Based Modelling

Michael Pedersen, Andrew Phillips, Gordon D Plotkin.
PLOS ONE (2015)
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Computational Design of Reaction-Diffusion Patterns Using DNA-Based Chemical Reaction Networks

Neil Dalchau, Georg Seelig, Andrew Phillips.
DNA Computing and Molecular Programming (DNA) (2014)
PDF Project

Abstract Modelling of Tethered DNA Circuits

Matthew R Lakin, Rasmus Petersen, Kathryn E Gray, Andrew Phillips.
DNA Computing and Molecular Programming (DNA) (2014)
PDF 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 (2014)
PDF Project

A Computational Method for Automated Characterization of Genetic Components

Boyan Yordanov, Neil Dalchau, Paul K Grant, Michael Pedersen, Stephen Emmott, Jim Haseloff, Andrew Phillips.
ACS Synthetic Biology (2014)
PDF Project

Bio Simulators: a web UI for biological simulation.

Michael Pedersen, Nicolas Oury, Colin Gravill, Andrew Phillips.
Bioinformatics (2014)
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Compiling DNA Strand Displacement Reactions Using a Functional Programming Language

Matthew R Lakin, Andrew Phillips.
Practical Aspects of Declarative Languages (PADL) (2014)
PDF Project

Programmable chemical controllers made from DNA

Yuan-Jyue Chen, Neil Dalchau, Niranjan Srinivas, Andrew Phillips, Luca Cardelli, David Soloveichik, Georg Seelig.
Nature Nanotechnology (2013)
PDF Project
Programmable chemical controllers made from DNA

Modular Verification of DNA Strand Displacement Networks via Serializability Analysis

Matthew R Lakin, Andrew Phillips, Darko Stefanovic.
DNA Computing and Molecular Programming (DNA) (2013)
PDF Project

Functional Analysis of Large-Scale DNA Strand Displacement Circuits

Boyan Yordanov, Christoph M Wintersteiger, Youssef Hamadi, Andrew Phillips, Hillel Kugler.
DNA Computing and Molecular Programming (2013)
PDF Project

Towards the rational design of synthetic cells with prescribed population dynamics

Neil Dalchau, Matthew J Smith, Samuel Martin, James R Brown, Stephen Emmott, Andrew Phillips.
Journal of The Royal Society Interface (2012)
PDF Project

Computational Modeling of Synthetic Microbial Biofilms

Timothy J Rudge, Paul J Steiner, Andrew Phillips, Jim Haseloff.
ACS Synthetic Biology (2012)
PDF 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 (2012)
PDF Project

Stochastic simulation of multiple process calculi for biology

Matthew R Lakin, Loïc Paulevé, Andrew Phillips.
Theoretical Computer Science (2012)
PDF Project

Abstractions for DNA circuit design

Matthew R Lakin, Simon Youssef, Luca Cardelli, Andrew Phillips.
Journal of The Royal Society Interface (2012)
PDF Project

Visual DSD: a design and analysis tool for DNA strand displacement systems

Matthew R Lakin, Simon Youssef, Filippo Polo, Stephen Emmott, Andrew Phillips.
Bioinformatics (2011)
PDF 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 (2011)
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Modelling, Simulating and Verifying Turing-Powerful Strand Displacement Systems

Matthew Lakin, Andrew Phillips.
DNA Computing and Molecular Programming (2011)
PDF Project

Localized Hybridization Circuits

Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif.
DNA Computing and Molecular Programming (DNA) (2011)
PDF Project

High-Level Programming Languages for Biomolecular Systems

Jacob Beal, Andrew Phillips, Douglas Densmore, Yizhi Cai.
Design and Analysis of Biomolecular Circuits (2011)
PDF Project

A generic abstract machine for stochastic process calculi

Loïc Paulevé, Simon Youssef, Matthew R Lakin, Andrew Phillips.
Computational Methods in Systems Biology (CMSB) (2010)
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The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding

Andrew Van Hateren, Edd James, Alistair Bailey, Andrew Phillips, Neil Dalchau, Tim Elliott.
Tissue Antigens (2010)
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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 (2009)
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A process model of Rho GTP-binding proteins

Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanoğulları, Andrew Phillips.
Theoretical Computer Science (2009)
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Towards programming languages for genetic engineering of living cells

Michael Pedersen, Andrew Phillips.
Journal of The Royal Society Interface (2009)
PDF Project
Towards programming languages for genetic engineering of living cells

A programming language for composable DNA circuits

Andrew Phillips, Luca Cardelli.
Journal of The Royal Society Interface (2009)
PDF Project
A programming language for composable DNA circuits

A Process Model of Actin Polymerisation

Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanoğulları, Andrew Phillips.
Electronic Notes in Theoretical Computer Science (2009)
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An Abstract Machine for the Stochastic Bioambient calculus

Andrew Phillips.
Electronic Notes in Theoretical Computer Science (2009)
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A Visual Process Calculus for Biology

Andrew Phillips.
Symbolic Systems Biology: Theory and Methods (2009)
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Compositionality, stochasticity, and cooperativity in dynamic models of gene regulation

Ralf Blossey, Luca Cardelli, Andrew Phillips.
HFSP Journal (2008)
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A Chart Semantics for the Pi-Calculus

Johannes Borgström, Andrew D Gordon, Andrew Phillips.
Electronic Notes in Theoretical Computer Science (2008)
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Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus

Andrew Phillips, Luca Cardelli.
Computational Methods in Systems Biology (CMSB) (2007)
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A Graphical Representation for Biological Processes in the Stochastic pi-Calculus

Andrew Phillips, Luca Cardelli, Giuseppe Castagna.
Transactions on Computational Systems Biology (2006)
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A Compositional Approach to the Stochastic Dynamics of Gene Networks

Ralf Blossey, Luca Cardelli, Andrew Phillips.
Transactions on Computational Systems Biology (2006)
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Specifying and Implementing Secure Mobile Applications in the Channel Ambient System

Andrew Phillips.
PhD Thesis (2005)
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A Distributed Abstract Machine for Boxed Ambient Calculi

Andrew Phillips, Nobuko Yoshida, Susan Eisenbach.
European Symposium on Programming (ESOP) (2004)
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