Emre Özdemir

The paper engineers Pseudomonas putida to strictly metabolize methanol through seven mutations, enabling growth on methanol as the sole carbon source.

The paper updates the iModulon decomposition of Bacillus subtilis transcriptomes using 782 RNAseq samples, revealing 142 iModulons that capture 80% of expression variance and provide new insights into gene regulation.

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 uses independent component analysis to characterize the transcriptional regulatory network of Streptomyces albidoflavus and identifies iModulons that describe its activity across growth conditions.

This study identifies novel transcriptional responses to protein production stress in E. coli using transcriptomic analytics and applies findings to optimize protein production.

The paper reconstructs and validates a genome-scale metabolic model for Lactobacillus reuteri JCM 1112T, demonstrating its accuracy in predicting metabolic behavior and identifying strategies for metabolic engineering.