Douglas McCloskey

Talk2Biomodels provides an AI platform for interacting with biological models using natural language, enhancing accessibility and FAIR principles.

This study shows that bioenergetic stress from antibiotic treatment enhances antimicrobial resistance and persistence in E. coli through increased ROS, repair mechanisms, and stringent response activation.

This study uses variational autoencoders to disentangle factors in tandem mass spectrometry data, enabling better interpretation and comparison across instruments.

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

SmartPeak automates metabolomics data processing with algorithms for alignment, calibration, and peak integration, improving reproducibility and throughput.

This study uses adaptive laboratory evolution to reveal divergent transcriptomic and metabolomic adaptations in E. coli knockout strains with similar initial perturbations.

The paper shows how multiple optimal phenotypes emerge in Escherichia coli pgi knockout strains through adaptive evolution, overcoming redox and metabolite imbalances.