Colton J. Lloyd

The paper presents a computational workflow to design enzyme selection systems (ESSs) that couple enzyme activity to microbial metabolism, creating a database of 25,505 ESS designs for Escherichia coli.

The paper analyzes enterobacterial genomes to identify secondary metabolite gene clusters, finding 8604 BGCs across 2627 genomes and associating some with specific biological functions.

The paper uses genome-scale models to compute proteome allocation under different conditions, revealing variability in cofactor use and protein composition for E. coli growth.

The paper estimates in vivo enzyme turnover numbers (kcats) in E. coli using metabolic specialist strains and shows their stability and predictive power over in vitro kcats.

This paper designs and evolves synthetic syntrophic E. coli pairs using a novel algorithm, revealing metabolic changes that enhance community fitness and guide co-culture optimization.

DynamicME simulates and refines integrated metabolism and protein expression models using time-course data, accurately predicting substrate utilization and expression profiles.

The paper develops a quantitative framework to predict ROS stress responses in E. coli across molecular, network, and genetic levels.

COBRAme is a software framework for building and simulating ME-models, enabling efficient reconstruction and analysis of genome-scale models of metabolism and gene expression.

BOFdat generates biomass objective function stoichiometric coefficients from omic data and calculates maintenance costs.