Jerome Bonnet

A scalable architecture for tuning multistate differentiation ratios in synthetic microbial consortia

This paper introduces a synthetic biology framework that enables tunable differentiation ratios in microbial consortia, validated in a mouse tumor model.

Split minireporters facilitate monitoring of gene expression and peptide production in linear cell-free transcription-translation systems

This paper introduces minireporters for monitoring gene expression and peptide production in cell-free systems, reducing DNA length and synthesis costs while maintaining reliable output.

LactoSpanks: a collection of IPTG inducible promoters for the commensal lactic acid bacteria Lactobacillus gasseri.

The paper introduces LactoSpanks, a set of IPTG-inducible promoters for Lactobacillus gasseri, offering tunable expression with reduced leakage and improved dynamic range.

Evaluating and mitigating clinical samples matrix effects on TX-TL cell-free performance

The paper evaluates matrix effects on cell-free biosensor performance in clinical samples and introduces a method to mitigate these effects using a modified RNase inhibitor.

PeroxiHUB: a modular cell-free biosensing platform using H2O2 as signal integrator

PeroxiHUB is a cell-free biosensing platform that detects metabolites by converting them into H2O2 using enzymatic transducers, enabling modular and scalable detection.

Rapid prototyping of metabolites detection by bacterial biosensors in human fecal samples.

This paper develops a method to detect gut metabolites in human fecal samples using bacterial biosensors, showing their sensitivity and the need for individual optimization.

Differentially optimized cell-free buffer enables robust expression from unprotected linear DNA in exonuclease-deficient extracts

This paper develops exonuclease-deficient cell-free extracts and optimized buffers to enable robust expression from unprotected linear DNA without additional protection strategies.

A synthetic receptor platform enables rapid and portable monitoring of liver dysfunction via engineered bacteria.

This paper introduces a synthetic receptor platform for detecting liver dysfunction biomarkers using engineered bacteria, achieving sensitive and portable diagnostics.

An engineered lactate responding promoter system operating in glucose-rich and anaerobic environments.

The paper engineers a lactate biosensor system that functions in glucose-rich and anaerobic environments by modifying a natural promoter.

Rational programming of history-dependent logic in cellular populations.

This paper presents systematic and automated frameworks for implementing robust history-dependent genetic programs in cellular populations.

Exploring the design space of recombinase logic circuits.

The paper explores the design space of recombinase-based logic circuits by generating and analyzing millions of designs to identify effective architectures for implementing logic functions.

Metabolic Perceptrons for Neural Computing in Biological Systems

The paper introduces metabolic perceptrons for binary classification of metabolite combinations using computational models and experimental validation in synthetic biological circuits.

Plug-and-Play Metabolic Transducers Expand the Chemical Detection Space of Cell-Free Biosensors

This paper introduces hybrid cell-free biosensors that expand the range of detectable chemicals by combining synthetic metabolic cascades with transcription factor-based networks.

Hierarchical composition of reliable recombinase logic devices.

This paper presents a framework for building reliable recombinase logic devices using hierarchical composition of optimized switches, enabling up to 4-input Boolean logic control of cellular behavior.

Analytic framework for stochastic binary biological switches

The paper develops an analytic framework to study stochastic dynamics of binary biological switches and identifies two operating regimes with distinct distribution patterns.