Programming DNA Circuits

Established: February 7, 2009

Publications

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- A deep learning model for predicting next-generation sequencing depth from DNA sequence
  
  Jinny X. Zhang, Boyan Yordanov, Alexander Gaunt, Michael X. Wang, Peng Dai, Yuan-Jyue Chen, Kerou Zhang, John Z. Fang, Neil Dalchau, Jiaming Li, Andrew Phillips, David Yu Zhang
  
  Nature Communications | July 2021, Vol 12
  
  Publication Project
- 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