Stefano Donati

This study improves acetate tolerance in Pseudomonas putida through adaptive laboratory evolution and identifies gacA and fabB as key targets for efficient acetate assimilation.

The paper uses automated mini-bioreactors to study the temporal dynamics and multi-omics responses of CRISPRi knockdowns in Pseudomonas putida, identifying a critical time window for phenotypic impact.

The paper presents a robust LC-MS/MS workflow for high-throughput metabolic profiling of bacteria using stable isotope dilution mass spectrometry.

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

This study investigates how Pseudomonas putida uses two transhydrogenases to maintain redox balance across different metabolic conditions, revealing their essential roles in growth and stress tolerance.

The paper introduces growthcurves, a Python package and web tools for analyzing biological growth curves with human-in-the-loop workflows, providing automated fitting and interactive inspection.

The paper identifies a recursive isoleucine biosynthesis pathway in E. coli driven by the promiscuous activity of acetohydroxyacid synthase II, using glyoxylate and pyruvate directly instead of threonine.

This paper curates and analyzes 22 genomes of Cupriavidus necator to assess genomic diversity and metabolic potential for one-carbon biomanufacturing, identifying three strains with promising traits.

The paper engineers Parageobacillus thermoglucosidasius to use methanol via the RuMP cycle for growth, achieving 17% biomass from methanol without heterologous enzyme expression.

This study attempts to engineer the reductive glycine pathway in Parageobacillus thermoglucosidasius for formate and methanol assimilation but finds limited success due to metabolic limitations and incomplete pathway implementation.

This paper presents a computational workflow for designing and testing E. coli metabolic sensors that detect glyoxylate and glycolate across a wide concentration range, with applications in bioengineering and environmental monitoring.

This paper engineers a synthetic C2 auxotrophy in Pseudomonas putida to enable alternative sugar catabolism via the phosphoketolase shunt, improving growth through metabolic rewiring.

The paper describes an automated workflow for generating high-throughput microbial multi-omics datasets and evaluates its effectiveness with three model organisms.