Richard M. Murray

The paper shows that PPC neurons encode hand-eye movements additively, allowing modular decoding of coordinated movements.

The paper develops a chemical reaction network model for PURE cell-free expression systems to predict protein synthesis kinetics using mass-action reactions.

The paper measures repression curves of genetic NOT gates in E. coli under growth and arrest conditions, finding growth arrest reduces unrepressed expression by >100-fold.

This study identifies a novel mechanism by which E. coli Nissle 1917 colonizes the nematode Steinernema hermaphroditum through immune cell interactions and cuticle persistence.

This study demonstrates a method to generate antigen-presenting vesicles displaying pMHCI using engineered constructs, which selectively stimulate T cells for potential cell-free immunotherapy.

This paper develops a coreactant-free ECL sensing platform with entwined spiral microelectrodes for sensitive, multiplexed POC diagnostics.

The paper develops a DNA part library for X. griffiniae to facilitate genetic circuit construction and characterize promoter and RBS strengths.

This paper introduces a communication-free method to stabilize microbial consortia using stochastic phase variation, demonstrating dynamic stability in 2- and 3-state consortia.

The paper develops a coarse-grained model of cell-free protein synthesis using metabolomics data and Bayesian inference to predict expression dynamics across novel conditions.

This study optimizes the One-Pot PURE system by addressing expression instability and proteolysis in E. coli strains, improving protein production efficiency.

This paper engineers a synthetic microbial circuit in E. coli to respond to two signals and secrete IL-22 for anti-inflammatory effects in a gut epithelial model.

This study shows that MGapt fluorescence in commercial PURE systems is unstable and influenced by chemical factors like DTT, leading to inaccurate RNA measurements and proposes a model to predict these effects.

This paper develops a field-deployable arsenic sensor using genetically modified Bacillus megaterium integrated with CMOS technology, achieving detection below EPA thresholds in soil and air.

This paper develops cell-free transcription-translation systems in three soil Pseudomonads, demonstrating their ability to characterize and engineer biological parts without genome integration.

The paper engineers a ratiometric bioreporter in Pseudomonas synxantha 2-79 to detect phosphorus limitation in soil, showing improved performance over native promoters and robustness across pH ranges.

TRILL enables scalable, modular deep-learning workflows for protein analysis and engineering by integrating models like ESM-2 and DiffDock.

The paper builds and validates a chemical reaction network model for PURE protein synthesis using mass-action reactions, accurately predicting mRNA and protein production dynamics.

This paper develops a framework for addressable and adaptable DNA messaging in engineered consortia, enabling targeted message transfer and dynamic recipient list updates.

The paper presents a pipeline for modeling and parameter identification in biological systems, applied to characterize integrase and excisionase activity in cell-free systems.

This study develops a differentiation circuit in E. coli to enhance the evolutionary stability of burdensome and toxic engineered functions through terminal differentiation.

This study demonstrates that layered feedback control in synthetic biomolecular networks in E. coli overcomes the robustness-efficiency trade-off, validating control theory predictions through experimental validation.

The paper introduces bioscrape, a Python package for fast and flexible simulation and parameter estimation of chemical reaction networks in synthetic biology.

This paper introduces an automated model reduction algorithm for synthetic biological circuits, demonstrating its use in designing a consortium population control circuit.

BioCRNpyler compiles chemical reaction networks from modular biochemical parts, enabling rapid model development and exploration across diverse contexts.

The paper introduces an assume-guarantee contract framework for formalizing and implementing biological circuit designs using ordinary differential equations.

This paper designs a synthetic mammalian circuit using auxin for population control, showing it limits growth more robustly than non-paradoxical designs.

The paper models dynamic transcriptional circuits using CRISPRi and identifies key parameters for their construction.

This paper demonstrates a genetic circuit that records small molecule concentration changes in living cells using CRISPR-Cas9 and integrase-mediated DNA integration.

The paper describes a stable DNA replication mechanism for synthetic genetic circuits and explains its derivation from a mechanistic model of ColE1 replication.