Richard M Murray

Design of a Toolbox of RNA Thermometers

The paper designs a library of RNA thermometers with varying temperature responses, validated experimentally and computationally.

A cell-free framework for biological systems engineering

This paper demonstrates that synthetic gene networks can be designed, characterized, and engineered in a cell-free system and successfully transferred to living cells, showing their applicability in both in vitro and in vivo contexts.

The effects of time-varying temperature on delays in genetic networks

This paper analyzes how time-varying temperature affects delays in genetic networks and shows that temperature entrainment can occur even with temperature compensation mechanisms.

Characterizing and Prototyping Genetic Networks with Cell-Free Transcription-Translation Reactions

This paper demonstrates the use of cell-free TX-TL systems to rapidly characterize genetic networks, including an RNA transcriptional cascade and a protein-regulated incoherent feed-forward loop.

Engineering Transcriptional Regulator Effector Specificity using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor

This study designs and screens qacR variants to create a vanillin sensor using computational methods and in vitro testing, identifying two mutants that respond to vanillin in both in vitro and in vivo settings.

An analytical approach to bistable biological circuit discrimination using real algebraic geometry

This paper uses real algebraic geometry to analyze bistable biological circuits, showing how topological properties affect parameter space and demonstrating the utility of Sturms theorem over traditional methods.

Population diversification in a yeast metabolic program promotes anticipation of environmental shifts

The paper shows that yeast populations activate the galactose pathway before glucose is fully consumed, enabling faster metabolic transitions and a fitness advantage.

Synthetic logic circuits using RNA aptamer against T7 RNA polymerase

This paper demonstrates the use of an RNA aptamer against T7 RNA polymerase to create synthetic logic circuits and transcriptional cascades in E. coli.

Negative autoregulation matches production and demand in synthetic transcriptional networks

This paper introduces a negative autoregulation system for synthetic genelets that matches production and demand, showing improved robustness and scalability compared to cross-activation.

A Scalable Formulation for Engineering Combination Therapies for Evolutionary Dynamics of Disease

The paper develops a scalable algorithm for designing combination therapies that stabilize disease evolutionary dynamics using optimization with regularization.

Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems

This study uses cell-free TX-TL systems to rapidly prototype and characterize RNA genetic circuits, showing response times of ~5 minutes per cascade step and demonstrating temporal gene expression staging.

Design and implementation of a synthetic biomolecular concentration tracker

This paper designs and implements a synthetic biomolecular concentration tracker in E. coli that tracks input protein concentration in real time using a feedback loop.