Andrew Phillips

Latest

• Automated Leak Analysis of Nucleic Acid Circuits
• A deep learning model for predicting next-generation sequencing depth from DNA sequence
• Interpretation of morphogen gradients by a synthetic bistable circuit
• Domain-Specific Programming Languages for Computational Nucleic Acid Systems
• Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms
• Fast Enumeration of Non-isomorphic Chemical Reaction Networks
• A Logic Programming Language for Computational Nucleic Acid Devices
• Efficient Amortised Bayesian Inference for Hierarchical and Nonlinear Dynamical Systems
• DNA-based communication in populations of synthetic protocells
• Escherichia coli can survive stress by noisy growth modulation
• Predicting DNA hybridization kinetics from sequence
• Synthesizing and tuning stochastic chemical reaction networks with specified behaviours
• A Mechanistic Model for Predicting Cell Surface Presentation of Competing Peptides by MHC Class I Molecules
• Automated analysis of tethered DNA nanostructures using constraint solving
• Computing with biological switches and clocks
• Automated, Constraint-Based Analysis of Tethered DNA Nanostructures
• A spatially localized architecture for fast and modular DNA computing
• A strand graph semantics for DNA-based computation
• Modular verification of chemical reaction network encodings via serializability analysis
• Characterization of Intrinsic Properties of Promoters
• Orthogonal intercellular signaling for programmed spatial behavior.
• Selector function of MHC I molecules is determined by protein plasticity
• Probabilistic Analysis of Localized DNA Hybridization Circuits
• A High-Level Language for Rule-Based Modelling
• Abstract Modelling of Tethered DNA Circuits
• Computational Design of Reaction-Diffusion Patterns Using DNA-Based Chemical Reaction Networks
• A Computational Method for Automated Characterization of Genetic Components
• Computational Design of Nucleic Acid Feedback Control Circuits
• Bio Simulators: a web UI for biological simulation.
• Compiling DNA Strand Displacement Reactions Using a Functional Programming Language
• Programmable chemical controllers made from DNA
• Functional Analysis of Large-Scale DNA Strand Displacement Circuits
• Modular Verification of DNA Strand Displacement Networks via Serializability Analysis
• Towards the rational design of synthetic cells with prescribed population dynamics
• Computational Modeling of Synthetic Microbial Biofilms
• Design and analysis of DNA strand displacement devices using probabilistic model checking
• Stochastic simulation of multiple process calculi for biology
• Abstractions for DNA circuit design
• Visual DSD: a design and analysis tool for DNA strand displacement systems
• A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization
• Localized Hybridization Circuits
• Modelling, Simulating and Verifying Turing-Powerful Strand Displacement Systems
• High-Level Programming Languages for Biomolecular Systems
• A generic abstract machine for stochastic process calculi
• The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding
• Computational modeling of the EGFR network elucidates control mechanisms regulating signal dynamics
• A process model of Rho GTP-binding proteins
• A programming language for composable DNA circuits
• Towards programming languages for genetic engineering of living cells
• A Process Model of Actin Polymerisation
• An Abstract Machine for the Stochastic Bioambient calculus
• A Visual Process Calculus for Biology
• Compositionality, stochasticity, and cooperativity in dynamic models of gene regulation
• A Chart Semantics for the Pi-Calculus
• Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus
• A Compositional Approach to the Stochastic Dynamics of Gene Networks
• A Graphical Representation for Biological Processes in the Stochastic pi-Calculus
• Specifying and Implementing Secure Mobile Applications in the Channel Ambient System
• A Distributed Abstract Machine for Boxed Ambient Calculi