Station B

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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