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, 巻12

Publication プロジェクト

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, 巻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, 巻11(5545)

Publication プロジェクト

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, 巻82(136)

Publication Publication プロジェクト

Domain-specific programming languages for computational nucleic acid systems

Matthew R. Lakin, Andrew Phillips

ACS Synthetic Biology | June 2020, 巻9(7): pp. 1499-1513

Publication プロジェクト

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, 巻11: pp. 950

Publication プロジェクト

Fast enumeration of non-isomorphic chemical reaction networks

Carlo Spaccasassi, Boyan Yordanov, Andrew Phillips, Neil Dalchau

Computational Methods for Systems Biology (CMSB) | September 2019

編集者: 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 プロジェクト プロジェクト

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 プロジェクト

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, 巻e100003

DOI Publication プロジェクト

A Logic Programming Language for Computational Nucleic Acid Devices

Carlo Spaccasassi, Matthew R. Lakin, Andrew Phillips

ACS Synthetic Biology | October 2018

Publication プロジェクト

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, 巻53(33)

Publication プロジェクト

Formal Analysis of Network Motifs

Hillel Kugler, Sara-Jane Dunn, Boyan Yordanov

CMSB | September 2018

Publication DOI プロジェクト

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

公開日 公開日 プロジェクト プロジェクト

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, 巻9: pp. 1538

公開日 公開日 プロジェクト

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

公開日 公開日 プロジェクト プロジェクト

Model reduction enables Turing instability analysis of large reaction–diffusion models

Stephen Smith, Neil Dalchau

Journal of the Royal Society Interface | March 2018, 巻15

公開日 公開日 プロジェクト

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 プロジェクト プロジェクト

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, 巻7: pp. 14367

公開日 公開日 プロジェクト

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, 巻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

公開日 公開日 プロジェクト

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

公開日 公開日 プロジェクト

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 プロジェクト

Efficient Switches in Biology and Computer Science

Luca Cardelli, Rosa D Hernansaiz-Ballesteros, Neil Dalchau, Attila Csikasz-Nagy

PLoS Computational Biology | January 2017, 巻13: pp. e1005100

公開日 公開日 公開日

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

公開日 公開日

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, 巻2

公開日 公開日

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

公開日 プロジェクト

A strand graph semantics for DNA-based computation

Rasmus Petersen, Matthew R Lakin, Andrew Phillips

Theoretical Computer Science | June 2016, 巻632: pp. 43-73

Publication Publication プロジェクト

Modular verification of chemical reaction network encodings via serializability analysis

Matthew R Lakin, Darko Stefanovic, Andrew Phillips

Theoretical Computer Science | June 2016, 巻632: pp. 21

Publication プロジェクト

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, 巻146: pp. 26-34

公開日 公開日 公開日

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, 巻27: pp. 1863-1874

公開日 公開日

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

公開日 プロジェクト

Noise Reduction in Complex Biological Switches

Attila Csikasz-Nagy, Neil Dalchau, Mirco Tribastone, Max Tschaikowski, Luca Cardelli

Scientific Reports | February 2016, 巻6: pp. 20214

公開日 公開日

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, 巻5: pp. 14928

公開日 公開日 プロジェクト

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

公開日 公開日 プロジェクト

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, 巻9211

公開日 公開日 公開日 プロジェクト

Probabilistic analysis of localized DNA hybridization circuits

Neil Dalchau, Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif

ACS Synthetic Biology | June 2015, 巻4: pp. 898-913

Publication Publication プロジェクト

A High-Level Language for Rule-Based Modelling

Michael Pedersen, Andrew Phillips, Gordon D. Plotkin

PLoS ONE | June 2015, 巻10(6): pp. e0114296

公開日

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, 巻205: pp. 918-927

公開日

What makes a biological clock efficient?

Attila Csikász-Nagy, Neil Dalchau

MSR-TR-2014-134 | September 2014

Essays for the Luca Cardelli Fest

公開日

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

公開日 公開日 公開日 プロジェクト

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

公開日 公開日 公開日 プロジェクト

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 | Springer による投稿 | 2014 | A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations edition

公開日 公開日

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

公開日 公開日 公開日 プロジェクト

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, 巻3: pp. 600-616

公開日 公開日 プロジェクト

Defining an essential transcriptional factor program for naive pluripotency

Sara-Jane Dunn, Graziano Martello, Boyan Yordanov, Stephen Emmott, Austin Smith

Science | June 2014, 巻344: pp. 1156

Publication プロジェクト

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, 巻3(8): pp. 578-588

Publication Publication プロジェクト

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

公開日

Bio Simulators: a web UI for biological simulation

Michael Pedersen, Nicolas Oury, Andrew Phillips

Bioinformatics | January 2014, 巻30: pp. 1491-1492

公開日 公開日

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 プロジェクト

Biocharts: Unifying Biological Hypotheses with Models and Experiments

Hillel Kugler

IEEE 9th International Conference on e-Science | October 2013

公開日

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, 巻8: pp. 755-762

公開日 プロジェクト

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, 巻201(1): pp. 168-179

公開日

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

公開日 公開日 プロジェクト プロジェクト

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, 巻8141: pp. 133-146

公開日 公開日 公開日 プロジェクト

Automated Ratiometric Characterization using GEC

Paul Grant, Jim Haseloff, Stephen Emmott, Boyan Yordanov, Neil Dalchau, Andrew Phillips

International Workshop on Biodesign Automation | July 2013

公開日 プロジェクト

Z34Bio: An SMT-based Framework for Analyzing Biological Computation

Boyan Yordanov, Youssef Hamadi, Hillel Kugler, Christoph M. Wintersteiger

SMT'13 | July 2013

公開日 プロジェクト

SMT-based Analysis of Biological Computation

Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, Hillel Kugler

NASA Formal Methods Symposium 2013 | May 2013

公開日 プロジェクト

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

公開日

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

公開日

Computational Modeling of Synthetic Microbial Biofilms

Timothy J. Rudge, Paul J. Steiner, Andrew Phillips, Jim Haseloff

ACS Synthetic Biology | July 2012, 巻1: pp. 345-352

公開日 プロジェクト

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, 巻9: pp. 1470-1485

Publication プロジェクト

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

公開日

Stochastic Simulation of Multiple Process Calculi for Biology

Matthew R. Lakin, Loïc Paulevé, Andrew Phillips

Theoretical Computer Science | May 2012, 巻431: pp. 181-206

Publication Publication プロジェクト プロジェクト

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, 巻9: pp. 2883-2898

Publication プロジェクト

Z3-4Biology SMT-Based Analysis of Biological Computation

Boyan Yordanov, Youssef Hamadi, Hillel Kugler, Christoph M. Wintersteiger

MSR-TR-2012-31 | March 2012

公開日 プロジェクト

Abstractions for DNA circuit design

Matthew R Lakin, Simon Youssef, Luca Cardelli, Andrew Phillips

Journal of the Royal Society Interface | March 2012, 巻9(68): pp. 470-486

Publication Publication プロジェクト

Understanding biological timing using mechanistic and black-box models

Neil Dalchau

New Phytologist | March 2012, 巻193(4): pp. 852-858

公開日

A model of stem cell population dynamics: in-silico analysis and in-vivo validation

Hillel Kugler

Development | January 2012, 巻139: pp. 47

公開日 公開日 公開日

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

公開日

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, 巻27: pp. 3211-3213

Publication プロジェクト

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, 巻7(10): pp. e1002144

公開日 公開日 プロジェクト プロジェクト

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

公開日

Localized Hybridization Circuits

Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif

International Conference on DNA Computing and Molecular Programming | September 2011, 巻6937: pp. 64-83

公開日 公開日 公開日 プロジェクト

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 プロジェクト

Synthesizing Biological Theories

Hillel Kugler, Cory Plock, Andy Roberts

Computer Aided Verification (CAV'11) | July 2011

公開日 ダウンロード

Model Checking Using SMT and Theory of Lists

Aleksandar Milicevic, Hillel Kugler

Nasa Formal Methods Symposium | April 2011

Nasa Formal Methods Symposium

公開日 公開日

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

公開日

Ticking Over – Circadian Systems Across the Kingdoms of Life

Neil Dalchau, Alex AR Webb

Biochemist | February 2011, 巻33(1): pp. 12-15

公開日

Stochastic Simulation of Process Calculi for Biology

Andrew Phillips, Matthew R. Lakin, Loïc Paulevé

Electronic Proceedings in Theoretical Computer Science | November 2010

公開日 公開日 プロジェクト

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, 巻76(4): pp. 259

公開日 公開日 プロジェクト

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

公開日 公開日 プロジェクト

Modeling Alveolar Volume Changes During Periodic Breathing in Heterogeneously Ventilated Lungs

Sara-Jane Dunn, Jonathan P. Whiteley

Annals of Biomedical Engineering | September 2010, 巻38: pp. 2988-2999

公開日 公開日

Biocharts: A Visual Formalism for Complex Biological Systems

Hillel Kugler, Antti Larjo, David Harel

Journal of the Royal Society Interface | July 2010, 巻7: pp. 1015-1024

Published online December 2009

公開日 公開日

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

公開日

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, 巻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

公開日 公開日

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, 巻23: pp. 835-845

公開日

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

公開日 公開日

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, 巻3: pp. 118

Publication プロジェクト

A Process Model of Rho GTP-binding Proteins

Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanogullari, Andrew Phillips

Theoretical Computer Science | August 2009, 巻410: pp. 3166-3185

Publication Publication プロジェクト

Systems analyses of circadian networks

Katharine E. Hubbard, Fiona C. Robertson, Neil Dalchau, Alex A. R. Webb

Molecular Biosystems | August 2009, 巻5: pp. 1502-1511

公開日 公開日

A programming language for composable DNA circuits

Andrew Phillips, Luca Cardelli

Journal of the Royal Society Interface | June 2009, 巻6: pp. S419-S436

公開日 公開日 プロジェクト

Towards programming languages for genetic engineering of living cells

Michael Pedersen, Andrew Phillips

Journal of the Royal Society Interface | April 2009, 巻6: pp. S437-S450

公開日 公開日 公開日 プロジェクト

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

公開日 公開日

Controller Synthesis from LSC Requirements

Hillel Kugler, Cory Plock, Amir Pnueli

Fundamental Approaches to Software Engineering (FASE'09) | March 2009

公開日 公開日

A Process Model of Actin Polymerisation

Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanoğulları, Andrew Phillips

Electronic Notes in Theoretical Computer Science | February 2009, 巻229(1): pp. 127-144

Publication Publication プロジェクト

A Visual Process Calculus for Biology

Andrew Phillips

Symbolic Systems Biology: Theory and Methods | Jones and Bartlett Publishers による投稿 | 2009 | Symbolic Systems Biology: Theory and Methods edition

公開日 プロジェクト

An Abstract Machine for the Stochastic Bioambient Calculus

Andrew Phillips

Electronic Notes in Theoretical Computer Science | January 2009, 巻227: pp. 143-159

公開日 公開日 プロジェクト

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)

公開日

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, 巻12

Publication プロジェクト

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 プロジェクト プロジェクト

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, 巻12

Publication プロジェクト

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, 巻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, 巻11(5545)

Publication プロジェクト

Domain-specific programming languages for computational nucleic acid systems

Matthew R. Lakin, Andrew Phillips

ACS Synthetic Biology | June 2020, 巻9(7): pp. 1499-1513

Publication プロジェクト

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, 巻11: pp. 950

Publication プロジェクト

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 プロジェクト

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, 巻e100003

DOI Publication プロジェクト

A Logic Programming Language for Computational Nucleic Acid Devices

Carlo Spaccasassi, Matthew R. Lakin, Andrew Phillips

ACS Synthetic Biology | October 2018

Publication プロジェクト

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, 巻53(33)

Publication プロジェクト

Formal Analysis of Network Motifs

Hillel Kugler, Sara-Jane Dunn, Boyan Yordanov

CMSB | September 2018

Publication DOI プロジェクト

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, 巻9: pp. 1538

公開日 公開日 プロジェクト

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 プロジェクト プロジェクト

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, 巻7: pp. 14367

公開日 公開日 プロジェクト

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, 巻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

公開日 公開日 プロジェクト

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

公開日 公開日 プロジェクト

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 プロジェクト

Efficient Switches in Biology and Computer Science

Luca Cardelli, Rosa D Hernansaiz-Ballesteros, Neil Dalchau, Attila Csikasz-Nagy

PLoS Computational Biology | January 2017, 巻13: pp. e1005100

公開日 公開日 公開日

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

公開日 公開日

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, 巻2

公開日 公開日

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

公開日 プロジェクト

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, 巻146: pp. 26-34

公開日 公開日 公開日

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, 巻27: pp. 1863-1874

公開日 公開日

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 | Springer による投稿 | 2014 | A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations edition

公開日 公開日

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

公開日 公開日 公開日 プロジェクト

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

公開日

Biocharts: Unifying Biological Hypotheses with Models and Experiments

Hillel Kugler

IEEE 9th International Conference on e-Science | October 2013

公開日

Z34Bio: An SMT-based Framework for Analyzing Biological Computation

Boyan Yordanov, Youssef Hamadi, Hillel Kugler, Christoph M. Wintersteiger

SMT'13 | July 2013

公開日 プロジェクト

SMT-based Analysis of Biological Computation

Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, Hillel Kugler

NASA Formal Methods Symposium 2013 | May 2013

公開日 プロジェクト

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

公開日

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

公開日

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

公開日

Z3-4Biology SMT-Based Analysis of Biological Computation

Boyan Yordanov, Youssef Hamadi, Hillel Kugler, Christoph M. Wintersteiger

MSR-TR-2012-31 | March 2012

公開日 プロジェクト

A model of stem cell population dynamics: in-silico analysis and in-vivo validation

Hillel Kugler

Development | January 2012, 巻139: pp. 47

公開日 公開日 公開日

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

公開日

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

公開日

Synthesizing Biological Theories

Hillel Kugler, Cory Plock, Andy Roberts

Computer Aided Verification (CAV'11) | July 2011

公開日 ダウンロード

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, 巻76(4): pp. 259

公開日 公開日 プロジェクト

Modeling Alveolar Volume Changes During Periodic Breathing in Heterogeneously Ventilated Lungs

Sara-Jane Dunn, Jonathan P. Whiteley

Annals of Biomedical Engineering | September 2010, 巻38: pp. 2988-2999

公開日 公開日

Biocharts: A Visual Formalism for Complex Biological Systems

Hillel Kugler, Antti Larjo, David Harel

Journal of the Royal Society Interface | July 2010, 巻7: pp. 1015-1024

Published online December 2009

公開日 公開日

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, 巻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

公開日 公開日

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, 巻3: pp. 118

Publication プロジェクト

Controller Synthesis from LSC Requirements

Hillel Kugler, Cory Plock, Amir Pnueli

Fundamental Approaches to Software Engineering (FASE'09) | March 2009

公開日 公開日

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

公開日 公開日

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, 巻11(5545)

Publication プロジェクト

Automated, Constraint-Based Analysis of Tethered DNA Nanostructures

Matthew R. Lakin, Andrew Phillips

International Conference on DNA Computing and Molecular Programming | September 2017

公開日 公開日 プロジェクト

Noise Reduction in Complex Biological Switches

Attila Csikasz-Nagy, Neil Dalchau, Mirco Tribastone, Max Tschaikowski, Luca Cardelli

Scientific Reports | February 2016, 巻6: pp. 20214

公開日 公開日

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

公開日 公開日 公開日 プロジェクト

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

公開日 公開日 プロジェクト プロジェクト

Model Checking Using SMT and Theory of Lists

Aleksandar Milicevic, Hillel Kugler

Nasa Formal Methods Symposium | April 2011

Nasa Formal Methods Symposium

公開日 公開日

Stochastic Simulation of Process Calculi for Biology

Andrew Phillips, Matthew R. Lakin, Loïc Paulevé

Electronic Proceedings in Theoretical Computer Science | November 2010

公開日 公開日 プロジェクト

Accelerating Smart Play-Out

David Harel, Hillel Kugler, Shahar Maoz, Itai Segali

SOFSEM 2010: Theory and Practice of Computer Science | January 2010

公開日 公開日

A programming language for composable DNA circuits

Andrew Phillips, Luca Cardelli

Journal of the Royal Society Interface | June 2009, 巻6: pp. S419-S436

公開日 公開日 プロジェクト

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)

公開日

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, 巻82(136)

Publication Publication プロジェクト

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

公開日 公開日 プロジェクト プロジェクト

Model reduction enables Turing instability analysis of large reaction–diffusion models

Stephen Smith, Neil Dalchau

Journal of the Royal Society Interface | March 2018, 巻15

公開日 公開日 プロジェクト

A strand graph semantics for DNA-based computation

Rasmus Petersen, Matthew R Lakin, Andrew Phillips

Theoretical Computer Science | June 2016, 巻632: pp. 43-73

Publication Publication プロジェクト

Modular verification of chemical reaction network encodings via serializability analysis

Matthew R Lakin, Darko Stefanovic, Andrew Phillips

Theoretical Computer Science | June 2016, 巻632: pp. 21

Publication プロジェクト

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, 巻146: pp. 26-34

公開日 公開日 公開日

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

公開日 プロジェクト

Noise Reduction in Complex Biological Switches

Attila Csikasz-Nagy, Neil Dalchau, Mirco Tribastone, Max Tschaikowski, Luca Cardelli

Scientific Reports | February 2016, 巻6: pp. 20214

公開日 公開日

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, 巻5: pp. 14928

公開日 公開日 プロジェクト

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

公開日 公開日 プロジェクト

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, 巻9211

公開日 公開日 公開日 プロジェクト

Probabilistic analysis of localized DNA hybridization circuits

Neil Dalchau, Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif

ACS Synthetic Biology | June 2015, 巻4: pp. 898-913

Publication Publication プロジェクト

A High-Level Language for Rule-Based Modelling

Michael Pedersen, Andrew Phillips, Gordon D. Plotkin

PLoS ONE | June 2015, 巻10(6): pp. e0114296

公開日

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, 巻205: pp. 918-927

公開日

What makes a biological clock efficient?

Attila Csikász-Nagy, Neil Dalchau

MSR-TR-2014-134 | September 2014

Essays for the Luca Cardelli Fest

公開日

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

公開日 公開日 公開日 プロジェクト

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

公開日 公開日 公開日 プロジェクト

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 | Springer による投稿 | 2014 | A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations edition

公開日 公開日

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

公開日 公開日 公開日 プロジェクト

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, 巻3: pp. 600-616

公開日 公開日 プロジェクト

Defining an essential transcriptional factor program for naive pluripotency

Sara-Jane Dunn, Graziano Martello, Boyan Yordanov, Stephen Emmott, Austin Smith

Science | June 2014, 巻344: pp. 1156

Publication プロジェクト

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, 巻3(8): pp. 578-588

Publication Publication プロジェクト

Bio Simulators: a web UI for biological simulation

Michael Pedersen, Nicolas Oury, Andrew Phillips

Bioinformatics | January 2014, 巻30: pp. 1491-1492

公開日 公開日

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 プロジェクト

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, 巻8: pp. 755-762

公開日 プロジェクト

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, 巻201(1): pp. 168-179

公開日

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

公開日 公開日 プロジェクト プロジェクト

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, 巻8141: pp. 133-146

公開日 公開日 公開日 プロジェクト

Automated Ratiometric Characterization using GEC

Paul Grant, Jim Haseloff, Stephen Emmott, Boyan Yordanov, Neil Dalchau, Andrew Phillips

International Workshop on Biodesign Automation | July 2013

公開日 プロジェクト

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, 巻9: pp. 1470-1485

Publication プロジェクト

Computational Modeling of Synthetic Microbial Biofilms

Timothy J. Rudge, Paul J. Steiner, Andrew Phillips, Jim Haseloff

ACS Synthetic Biology | July 2012, 巻1: pp. 345-352

公開日 プロジェクト

Stochastic Simulation of Multiple Process Calculi for Biology

Matthew R. Lakin, Loïc Paulevé, Andrew Phillips

Theoretical Computer Science | May 2012, 巻431: pp. 181-206

Publication Publication プロジェクト プロジェクト

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, 巻9: pp. 2883-2898

Publication プロジェクト

Abstractions for DNA circuit design

Matthew R Lakin, Simon Youssef, Luca Cardelli, Andrew Phillips

Journal of the Royal Society Interface | March 2012, 巻9(68): pp. 470-486

Publication Publication プロジェクト

Understanding biological timing using mechanistic and black-box models

Neil Dalchau

New Phytologist | March 2012, 巻193(4): pp. 852-858

公開日

A model of stem cell population dynamics: in-silico analysis and in-vivo validation

Hillel Kugler

Development | January 2012, 巻139: pp. 47

公開日 公開日 公開日

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, 巻27: pp. 3211-3213

Publication プロジェクト

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, 巻7(10): pp. e1002144

公開日 公開日 プロジェクト プロジェクト

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 プロジェクト

Localized Hybridization Circuits

Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif

International Conference on DNA Computing and Molecular Programming | September 2011, 巻6937: pp. 64-83

公開日 公開日 公開日 プロジェクト

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

公開日

Ticking Over – Circadian Systems Across the Kingdoms of Life

Neil Dalchau, Alex AR Webb

Biochemist | February 2011, 巻33(1): pp. 12-15

公開日

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

公開日

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, 巻23: pp. 835-845

公開日

A Process Model of Rho GTP-binding Proteins

Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanogullari, Andrew Phillips

Theoretical Computer Science | August 2009, 巻410: pp. 3166-3185

Publication Publication プロジェクト

Systems analyses of circadian networks

Katharine E. Hubbard, Fiona C. Robertson, Neil Dalchau, Alex A. R. Webb

Molecular Biosystems | August 2009, 巻5: pp. 1502-1511

公開日 公開日

Towards programming languages for genetic engineering of living cells

Michael Pedersen, Andrew Phillips

Journal of the Royal Society Interface | April 2009, 巻6: pp. S437-S450

公開日 公開日 公開日 プロジェクト

A Process Model of Actin Polymerisation

Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanoğulları, Andrew Phillips

Electronic Notes in Theoretical Computer Science | February 2009, 巻229(1): pp. 127-144

Publication Publication プロジェクト

An Abstract Machine for the Stochastic Bioambient Calculus

Andrew Phillips

Electronic Notes in Theoretical Computer Science | January 2009, 巻227: pp. 143-159

公開日 公開日 プロジェクト

A Visual Process Calculus for Biology

Andrew Phillips

Symbolic Systems Biology: Theory and Methods | Jones and Bartlett Publishers による投稿 | 2009 | Symbolic Systems Biology: Theory and Methods edition

公開日 プロジェクト

Fast enumeration of non-isomorphic chemical reaction networks

Carlo Spaccasassi, Boyan Yordanov, Andrew Phillips, Neil Dalchau

Computational Methods for Systems Biology (CMSB) | September 2019

編集者: 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

公開日 公開日 プロジェクト

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

公開日 公開日 プロジェクト プロジェクト

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, 巻12

Publication プロジェクト

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, 巻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, 巻11(5545)

Publication プロジェクト

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, 巻82(136)

Publication Publication プロジェクト

Domain-specific programming languages for computational nucleic acid systems

Matthew R. Lakin, Andrew Phillips

ACS Synthetic Biology | June 2020, 巻9(7): pp. 1499-1513

Publication プロジェクト

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, 巻11: pp. 950

Publication プロジェクト

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 プロジェクト

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, 巻e100003

DOI Publication プロジェクト

A Logic Programming Language for Computational Nucleic Acid Devices

Carlo Spaccasassi, Matthew R. Lakin, Andrew Phillips

ACS Synthetic Biology | October 2018

Publication プロジェクト

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, 巻53(33)

Publication プロジェクト

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

公開日 公開日 プロジェクト プロジェクト

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, 巻9: pp. 1538

公開日 公開日 プロジェクト

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

公開日 公開日 プロジェクト プロジェクト

Model reduction enables Turing instability analysis of large reaction–diffusion models

Stephen Smith, Neil Dalchau

Journal of the Royal Society Interface | March 2018, 巻15

公開日 公開日 プロジェクト

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 プロジェクト プロジェクト

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, 巻7: pp. 14367

公開日 公開日 プロジェクト

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, 巻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

公開日 公開日 プロジェクト

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 プロジェクト

Efficient Switches in Biology and Computer Science

Luca Cardelli, Rosa D Hernansaiz-Ballesteros, Neil Dalchau, Attila Csikasz-Nagy

PLoS Computational Biology | January 2017, 巻13: pp. e1005100

公開日 公開日 公開日

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

公開日 公開日

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, 巻2

公開日 公開日

A strand graph semantics for DNA-based computation

Rasmus Petersen, Matthew R Lakin, Andrew Phillips

Theoretical Computer Science | June 2016, 巻632: pp. 43-73

Publication Publication プロジェクト

Modular verification of chemical reaction network encodings via serializability analysis

Matthew R Lakin, Darko Stefanovic, Andrew Phillips

Theoretical Computer Science | June 2016, 巻632: pp. 21

Publication プロジェクト

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, 巻146: pp. 26-34

公開日 公開日 公開日

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, 巻27: pp. 1863-1874

公開日 公開日

Noise Reduction in Complex Biological Switches

Attila Csikasz-Nagy, Neil Dalchau, Mirco Tribastone, Max Tschaikowski, Luca Cardelli

Scientific Reports | February 2016, 巻6: pp. 20214

公開日 公開日

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, 巻5: pp. 14928

公開日 公開日 プロジェクト

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

公開日 公開日 プロジェクト

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, 巻9211

公開日 公開日 公開日 プロジェクト

Probabilistic analysis of localized DNA hybridization circuits

Neil Dalchau, Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif

ACS Synthetic Biology | June 2015, 巻4: pp. 898-913

Publication Publication プロジェクト

A High-Level Language for Rule-Based Modelling

Michael Pedersen, Andrew Phillips, Gordon D. Plotkin

PLoS ONE | June 2015, 巻10(6): pp. e0114296

公開日

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, 巻205: pp. 918-927

公開日

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, 巻3: pp. 600-616

公開日 公開日 プロジェクト

Defining an essential transcriptional factor program for naive pluripotency

Sara-Jane Dunn, Graziano Martello, Boyan Yordanov, Stephen Emmott, Austin Smith

Science | June 2014, 巻344: pp. 1156

Publication プロジェクト

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, 巻3(8): pp. 578-588

Publication Publication プロジェクト

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

公開日

Bio Simulators: a web UI for biological simulation

Michael Pedersen, Nicolas Oury, Andrew Phillips

Bioinformatics | January 2014, 巻30: pp. 1491-1492

公開日 公開日

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, 巻8: pp. 755-762

公開日 プロジェクト

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, 巻201(1): pp. 168-179

公開日

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, 巻8141: pp. 133-146

公開日 公開日 公開日 プロジェクト

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

公開日

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

公開日

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, 巻9: pp. 1470-1485

Publication プロジェクト

Computational Modeling of Synthetic Microbial Biofilms

Timothy J. Rudge, Paul J. Steiner, Andrew Phillips, Jim Haseloff

ACS Synthetic Biology | July 2012, 巻1: pp. 345-352

公開日 プロジェクト

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

公開日

Stochastic Simulation of Multiple Process Calculi for Biology

Matthew R. Lakin, Loïc Paulevé, Andrew Phillips

Theoretical Computer Science | May 2012, 巻431: pp. 181-206

Publication Publication プロジェクト プロジェクト

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, 巻9: pp. 2883-2898

Publication プロジェクト

Abstractions for DNA circuit design

Matthew R Lakin, Simon Youssef, Luca Cardelli, Andrew Phillips

Journal of the Royal Society Interface | March 2012, 巻9(68): pp. 470-486

Publication Publication プロジェクト

Understanding biological timing using mechanistic and black-box models

Neil Dalchau

New Phytologist | March 2012, 巻193(4): pp. 852-858

公開日

A model of stem cell population dynamics: in-silico analysis and in-vivo validation

Hillel Kugler

Development | January 2012, 巻139: pp. 47

公開日 公開日 公開日

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

公開日

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, 巻27: pp. 3211-3213

Publication プロジェクト

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, 巻7(10): pp. e1002144

公開日 公開日 プロジェクト プロジェクト

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

公開日

Localized Hybridization Circuits

Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John Reif

International Conference on DNA Computing and Molecular Programming | September 2011, 巻6937: pp. 64-83

公開日 公開日 公開日 プロジェクト

Ticking Over – Circadian Systems Across the Kingdoms of Life

Neil Dalchau, Alex AR Webb

Biochemist | February 2011, 巻33(1): pp. 12-15

公開日

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, 巻76(4): pp. 259

公開日 公開日 プロジェクト

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

公開日 公開日 プロジェクト

Modeling Alveolar Volume Changes During Periodic Breathing in Heterogeneously Ventilated Lungs

Sara-Jane Dunn, Jonathan P. Whiteley

Annals of Biomedical Engineering | September 2010, 巻38: pp. 2988-2999

公開日 公開日

Biocharts: A Visual Formalism for Complex Biological Systems

Hillel Kugler, Antti Larjo, David Harel

Journal of the Royal Society Interface | July 2010, 巻7: pp. 1015-1024

Published online December 2009

公開日 公開日

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, 巻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, 巻23: pp. 835-845

公開日

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, 巻3: pp. 118

Publication プロジェクト

A Process Model of Rho GTP-binding Proteins

Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanogullari, Andrew Phillips

Theoretical Computer Science | August 2009, 巻410: pp. 3166-3185

Publication Publication プロジェクト

Systems analyses of circadian networks

Katharine E. Hubbard, Fiona C. Robertson, Neil Dalchau, Alex A. R. Webb

Molecular Biosystems | August 2009, 巻5: pp. 1502-1511

公開日 公開日

A programming language for composable DNA circuits

Andrew Phillips, Luca Cardelli

Journal of the Royal Society Interface | June 2009, 巻6: pp. S419-S436

公開日 公開日 プロジェクト

Towards programming languages for genetic engineering of living cells

Michael Pedersen, Andrew Phillips

Journal of the Royal Society Interface | April 2009, 巻6: pp. S437-S450

公開日 公開日 公開日 プロジェクト

A Process Model of Actin Polymerisation

Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanoğulları, Andrew Phillips

Electronic Notes in Theoretical Computer Science | February 2009, 巻229(1): pp. 127-144

Publication Publication プロジェクト

An Abstract Machine for the Stochastic Bioambient Calculus

Andrew Phillips

Electronic Notes in Theoretical Computer Science | January 2009, 巻227: pp. 143-159

公開日 公開日 プロジェクト

Fast enumeration of non-isomorphic chemical reaction networks

Carlo Spaccasassi, Boyan Yordanov, Andrew Phillips, Neil Dalchau

Computational Methods for Systems Biology (CMSB) | September 2019

編集者: 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 プロジェクト プロジェクト

Formal Analysis of Network Motifs

Hillel Kugler, Sara-Jane Dunn, Boyan Yordanov

CMSB | September 2018

Publication DOI プロジェクト

Automated, Constraint-Based Analysis of Tethered DNA Nanostructures

Matthew R. Lakin, Andrew Phillips

International Conference on DNA Computing and Molecular Programming | September 2017

公開日 公開日 プロジェクト

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

公開日 プロジェクト

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

公開日 プロジェクト

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

公開日 公開日 公開日 プロジェクト

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

公開日 公開日 公開日 プロジェクト

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

公開日 公開日 公開日 プロジェクト

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 プロジェクト

Biocharts: Unifying Biological Hypotheses with Models and Experiments

Hillel Kugler

IEEE 9th International Conference on e-Science | October 2013

公開日

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

公開日 公開日 プロジェクト プロジェクト

Automated Ratiometric Characterization using GEC

Paul Grant, Jim Haseloff, Stephen Emmott, Boyan Yordanov, Neil Dalchau, Andrew Phillips

International Workshop on Biodesign Automation | July 2013

公開日 プロジェクト

Z34Bio: An SMT-based Framework for Analyzing Biological Computation

Boyan Yordanov, Youssef Hamadi, Hillel Kugler, Christoph M. Wintersteiger

SMT'13 | July 2013

公開日 プロジェクト

SMT-based Analysis of Biological Computation

Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, Hillel Kugler

NASA Formal Methods Symposium 2013 | May 2013

公開日 プロジェクト

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 プロジェクト

Synthesizing Biological Theories

Hillel Kugler, Cory Plock, Andy Roberts

Computer Aided Verification (CAV'11) | July 2011

公開日 ダウンロード

Model Checking Using SMT and Theory of Lists

Aleksandar Milicevic, Hillel Kugler

Nasa Formal Methods Symposium | April 2011

Nasa Formal Methods Symposium

公開日 公開日

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

公開日

Stochastic Simulation of Process Calculi for Biology

Andrew Phillips, Matthew R. Lakin, Loïc Paulevé

Electronic Proceedings in Theoretical Computer Science | November 2010

公開日 公開日 プロジェクト

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

公開日

Accelerating Smart Play-Out

David Harel, Hillel Kugler, Shahar Maoz, Itai Segali

SOFSEM 2010: Theory and Practice of Computer Science | January 2010

公開日 公開日

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

公開日 公開日

Controller Synthesis from LSC Requirements

Hillel Kugler, Cory Plock, Amir Pnueli

Fundamental Approaches to Software Engineering (FASE'09) | March 2009

公開日 公開日

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

公開日 公開日

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)

公開日

What makes a biological clock efficient?

Attila Csikász-Nagy, Neil Dalchau

MSR-TR-2014-134 | September 2014

Essays for the Luca Cardelli Fest

公開日

Z3-4Biology SMT-Based Analysis of Biological Computation

Boyan Yordanov, Youssef Hamadi, Hillel Kugler, Christoph M. Wintersteiger

MSR-TR-2012-31 | March 2012

公開日 プロジェクト

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 | Springer による投稿 | 2014 | A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations edition

公開日 公開日

A Visual Process Calculus for Biology

Andrew Phillips

Symbolic Systems Biology: Theory and Methods | Jones and Bartlett Publishers による投稿 | 2009 | Symbolic Systems Biology: Theory and Methods edition

公開日 プロジェクト