James M. Carothers

This paper introduces cSAGE, a conjugation-based genome engineering platform that enables site-specific integration in transformation-resistant bacteria, demonstrating its utility in bioproduction pathway prototyping.

The paper introduces CRISPRi-assisted E. coli strains to improve cloning success for burdensome genetic constructs by reducing metabolic burden during cloning.

This study evaluates Bayesian Metabolic Control Analysis (BMCA) using synthetic networks, finding it requires flux and enzyme data for accurate predictions and fails to reliably infer elasticity values and allosteric regulation.

The paper introduces mapSPLiT, a pooled CRISPRa/i screening platform for bacteria, linking perturbations to single-cell transcriptomes and expanding regulatory networks in E. coli and P. putida.

This study systematically maps bacterial CRISPRa design rules and finds no synergistic activation, highlighting mechanistic differences from eukaryotic systems.

This paper engineers a carbon-conserving cell-free system in E. coli to produce malate from formate and bicarbonate, achieving a 15-fold increase in titer and reducing background reactions by 6-fold.

The paper designs guide RNA structures for CRISPRa to optimize multi-gene expression in bacterial metabolic pathways, achieving higher product titers and identifying pathway bottlenecks.

The paper develops CRISPR-Cas tools to independently control transcription and translation in E. coli, showing reduced polar effects with dCas13 and enabling multiplexed gene regulation for biosynthesis.

This study evaluates PAM-flexible dCas9 variants for bacterial CRISPR activation and repression, finding trade-offs between PAM flexibility and repression efficiency.

This study identifies strict target site requirements for effective CRISPRa in bacteria and demonstrates a dCas9 variant with expanded PAM specificity to overcome these limitations.

This paper designs and tests kinetically-controlled RNA aptamer ribosensors for improved ligand sensitivity and selectivity in microbial cultures.