Jeffrey E. Barrick

The paper introduces a dual chassis framework (DUET) to combine rational metabolic design with adaptive evolution, enabling robust microbial platform development.

The paper refactors the E. coli MccV type I secretion system into modular genetic parts for secreting small proteins and screens class II microcins from plant-associated bacteria.

The paper develops a genetic biosensor to monitor dsRNA levels in bacterial cells, enhancing RNAi design in symbionts.

The paper discovers that Snodgrassella alvi, a core bee gut bacterium, is naturally competent, enabling high rates of DNA transfer between strains, which has implications for its evolution and potential microbiome engineering applications.

This study identifies contingency loci in phages that generate genetic diversity through frameshift mutations, enabling bet-hedging against host defenses.

This study evolves Serratia symbiotica bacteria in lab conditions and finds that prophage reactivation and phage resistance dominate evolutionary changes, leading to reduced virulence in aphids.

This study identifies mutations acquired during the domestication of Acinetobacter baylyi ADP1, showing their impact on competence and metabolism in modern strains.

The paper describes engineered Acinetobacter baylyi biosensors that detect specific DNA sequences with high sensitivity.

The paper develops a stochastic gene expression model to quantify how codon usage bias affects burden and yield during protein overexpression in bacteria, finding an overoptimization domain that reduces yield.

This study identifies biofilm-forming adhesins in Snodgrassella alvi that are essential for its mutualistic colonization of the bee gut.

This study shows that simple sequence repeats in Bartonella bacteria drive adaptation to specific rodent hosts through frameshift mutations in adhesin genes.

The paper develops a one-step genome editing method for Snodgrassella alvi, enabling gene knockouts and insertions with high accuracy and validation of mutant phenotypes.

The paper measures the growth burden of 301 BioBricks in E. coli and finds that 19.6% reduce growth, with most burdens explained by gene expression resource diversion.

The paper identifies 217 uncatalogued genetic part variants in engineered plasmids, highlighting widespread and convergent changes that may affect scientific reproducibility.

This study shows that laboratory evolution can recover fitness lost in Acinetobacter baylyi strains with large deletions through mutations in deletion-specific targets and global post-transcriptional regulators.

The paper identifies proto-genes in E. coli by analyzing the LTEE dataset, showing non-genic sequences evolve transcription and translation, often due to promoter formation and chromosomal events.

CryptKeeper predicts and mitigates unintended gene expression in bacterial DNA sequences by analyzing translational burden and identifying off-target elements.

This paper describes a method to study gene function in bees using engineered gut bacteria to induce RNA interference, achieving up to 75% gene knockdown.

This study identifies the genomic basis of evolutionary novelties in the Glassy-Winged Sharpshooter, revealing novel genes, horizontal gene transfer, and symbiotic associations contributing to its adaptations.

This paper genetically engineers a culturable aphid symbiont, Serratia symbiotica CWBI-2.3T, to track its colonization and induce heterologous gene expression in aphids, enabling paratransgenesis applications.

The paper estimates the rate of gene conversions between rRNA operons in Escherichia coli by sequencing evolved lineages and finds a low, consistent rate across different genomic regions.

The paper improves genome engineering methods for Acinetobacter baylyi ADP1, achieving genome streamlining through targeted deletions and CRISPR-based validation.

This study presents a comprehensive transcriptomics and proteomics dataset of E. coli under 34 growth conditions, revealing differences between exponential and stationary phases and differential gene expression under specific stresses.

The paper analyzes PTMs in E. coli under glucose-limiting conditions, identifying novel targets and temporal patterns for specific modifications and suggesting a new biological function for N-terminal acetylation.

The paper analyzes 264 genomes from 12 Escherichia coli populations over 50,000 generations to study genome evolution dynamics and finds that most fixed mutations are beneficial, with neutral mutations accumulating at a constant rate.

This study tracks genetic evolution in Escherichia coli populations over 20,000 generations, revealing clonal interference, selective sweeps, and frequency-dependent interactions among mutations.

The paper predicts growth conditions of E. coli from metabolic fluxes using regularized multinomial regression and finds that metabolic end products and a small number of reactions are sufficient for accurate prediction.