Ali Ebrahim

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.

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

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.