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

Modular verification of chemical reaction network encodings via serializability analysis

A strand graph semantics for DNA-based computation

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

Computational Design of Reaction-Diffusion Patterns Using DNA-Based Chemical Reaction Networks

Abstract Modelling of Tethered DNA Circuits

Computational Design of Nucleic Acid Feedback Control Circuits

A Computational Method for Automated Characterization of Genetic Components

Bio Simulators: a web UI for biological simulation.

Compiling DNA Strand Displacement Reactions Using a Functional Programming Language

Programmable chemical controllers made from DNA

Modular Verification of DNA Strand Displacement Networks via Serializability Analysis

Functional Analysis of Large-Scale DNA Strand Displacement Circuits

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

Modelling, Simulating and Verifying Turing-Powerful Strand Displacement Systems

Localized Hybridization Circuits

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

Towards programming languages for genetic engineering of living cells

A programming language for composable DNA circuits

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 Graphical Representation for Biological Processes in the Stochastic pi-Calculus

A Compositional Approach to the Stochastic Dynamics of Gene Networks

A Distributed Abstract Machine for Boxed Ambient Calculi