Matthew R. Bennett

Fast, long-range intercellular signal propagation through growth assisted positive feedback

The paper constructs and tests synthetic circuits in E. coli to show that positive feedback-regulated secondary signals can propagate faster and farther than diffusion-limited signals.

Title: Engineering Plasmids with Synthetic Origins of Replication

The paper designs synthetic origins of replication (SynORI) that allow customizable and modular plasmid copy numbers and environmental signal responses in E. coli.

Long-term homeostasis in microbial consortia via auxotrophic cross-feeding

This paper presents a method to control microbial consortium proportions using auxotrophic cross-feeding in continuous culture, demonstrating precise regulation through exogenous nutrient addition and mathematical modeling.

Pattern formation and bistability in a synthetic intercellular genetic toggle

This study creates a synthetic genetic toggle switch that exhibits population bistability and generates spatial differentiation patterns in bacterial colonies.

Tunable dynamics in a multi-straintranscriptional pulse generator

This paper demonstrates how to tune gene circuit dynamics in a synthetic microbial consortium by adjusting strain fractions, creating a pulse generator with controllable amplitude.

A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria

This paper designs a portable regulatory RNA array for tunable gene regulation across diverse bacteria, enabling complex circuitry without requiring large regulatory libraries.

Indirect enrichment of desirable, but less fit phenotypes, from a synthetic microbial community using microdroplet confinement

The paper demonstrates how microdroplet confinement can indirectly enrich a rare producer strain in a synthetic microbial community through spatial structure and metabolite diffusion.

Stochastic Neural Networks for Automatic Cell Tracking in Microscopy Image Sequences of Bacterial Colonies

This paper introduces a stochastic neural network method for tracking bacterial cell motion in microscopy sequences, achieving high registration accuracy in both simulated and experimental data.

RNA compensation: A positive feedback insulation strategy for RNA-based networks

This paper introduces RNA compensation, a positive feedback strategy to mitigate RNA signal consumption in RNA-based circuits, improving composability and modularity.

A synthetic system for asymmetric cell division in Escherichia coli

This paper describes a synthetic genetic circuit in E. coli that enables asymmetric cell division through plasmid partitioning, leading to differentiated daughter cells.

Spatiotemporal dynamics of synthetic microbial consortia in microfluidic devices

This study investigates how trap size in microfluidic devices affects the spatiotemporal dynamics of synthetic microbial consortia, revealing a trade-off between signaling effectiveness and strain proportion stability.

Bayesian inference of distributed time delay in transcriptional and translational regulation

The paper introduces a Bayesian framework to infer reaction rates and delay distributions in biochemical networks using single-cell data, showing robust parameter estimation with limited measurements.

Boundary-Driven Emergent Spatiotemporal Order in Growing Microbial Colonies

The paper introduces a stochastic spatial Moran model to explain spatiotemporal patterns in growing bacterial colonies, showing how boundary effects and cell-cell interactions drive alignment changes.

Modeling mechanical interactions in growing populations of rod-shaped bacteria

The paper presents an agent-based model to simulate mechanical interactions in growing rod-shaped bacterial populations and demonstrates its application in microfluidic traps.