Programming DNA 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 | July 2021, Vol 12

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

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 Logic Programming Language for Computational Nucleic Acid Devices

Carlo Spaccasassi, Matthew R. Lakin, Andrew Phillips

ACS Synthetic Biology | October 2018

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 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

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

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 Logic Programming Language for Computational Nucleic Acid Devices

Carlo Spaccasassi, Matthew R. Lakin, Andrew Phillips

ACS Synthetic Biology | October 2018

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

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

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 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 Logic Programming Language for Computational Nucleic Acid Devices

Carlo Spaccasassi, Matthew R. Lakin, Andrew Phillips

ACS Synthetic Biology | October 2018

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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