Richard M. Murray

The Compositional Encoding of Hand-Eye Coordinated Movements for Single Neurons in the Posterior Parietal Cortex

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

Nucleotide-level chemical reaction network modeling enables quantitative prediction of reconstituted cell-free expression system

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

Quantitative measurement of synthetic repression curves reveals design challenges for genetic circuit engineering under growth arrest

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.

Escherichia coli Nissle 1917 occupies previously undocumented host niches in the insect-parasitic nematode Steinernema hermaphroditum

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

Recruiting ESCRT to single-chain heterotrimer peptide-MHCI releases antigen-presenting vesicles that stimulate T cells selectively

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.

Highly Efficient Coreactant-Free Electrochemiluminescence Sensing Platform Using Novel Microfabricated Multiplexed Entwined Spiral Microelectrodes for Point-of-Care Applications

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

A DNA part library for reliable engineering of the emerging model nematode symbiotic bacterium Xenorhabdus griffiniae HGB2511

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

Synthetic Phase Variation for Engineered Microbial Consortia

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

Metabolomics-informed coarse-grained model enables prediction of cell-free protein expression dynamics

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.

Optimizing protein production in the One-Pot PURE system: insights into reaction composition and expression efficiency

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

Diagnostic and Therapeutic Microbial Circuit with Application to Intestinal Inflammation

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.

Metabolic perturbations to an E. coli-based cell-free system reveal a trade-off between transcription and translation

Impact of Chemical Dynamics of Commercial PURE Systems on Malachite Green Aptamer Fluorescence

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.

A Field-Deployable Arsenic Sensor Integrating Bacillus Megaterium with CMOS Technology

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.

Development of cell-free transcription-translation systems in three soil Pseudomonads

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

Engineering the soil bacterium Pseudomonas synxantha 2-79 into a ratiometric bioreporter for phosphorus limitation

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: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering

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

A chemical reaction network model of PURE

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.

Addressable and adaptable intercellular communication via DNA messaging

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

Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline

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

Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli

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

Layered Feedback Control Overcomes Performance Trade-off in Synthetic Biomolecular Networks

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.

Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape

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

An automated model reduction tool to guide the design and analysis of synthetic biological circuits

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

BioCRNpyler: Compiling Chemical Reaction Networks from Biomolecular Parts in Diverse Contexts

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

From Specification to Implementation: Assume-Guarantee Contracts for Synthetic Biology

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

Synthetic mammalian signaling circuits for robust cell population control

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

Modeling Dynamic Transcriptional Circuits with CRISPRi

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

Proof of concept continuous event logging in living cells

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

How to model DNA replication in stochastic models of synthetic genetic circuits (and why)

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