Ian A. Lewis

The paper shows that biomanufacturing conditions alter molecular states in hiPSCs without losing pluripotency, linking these changes to developmental programs.

LAMPrEY is a Python-based quality control tool for large-scale proteomics datasets that automates processing and analysis with MaxQuant and RawTools, enabling reproducible and rapid data interpretation.

This study identifies microbiome-derived hydroxyphenyl propanoates (HPPs) that enhance antitumour immunity by boosting gasdermin D activity in myeloid cells, improving immune checkpoint therapy outcomes in mice and correlating with better responses in human melanoma patients.

This study shows that Pseudomonas aeruginosa mutants lacking the H3-T6SS exploit itaconate to persist in phagocytes, enhancing their ability to cause chronic lung infections.

This study shows that P. aeruginosa sequesters itaconate by binding it to RpoN, enhancing its metabolic adaptation and promoting pulmonary infection.

This study shows that fumarate, regulated by host and pathogen, limits S. aureus growth by blocking metabolic pathways, while FumC enables adaptation through fumarate degradation and utilization.

The paper develops TUNA, an LC-MS system for time-resolved metabolomics of cultured cells, and uses it to identify novel metabolic phenotypes in uropathogens.

The paper surveys the metabolic activities of common uropathogenic bacteria in human urine using LC-MS, identifying four distinct metabolic clades.

DigestR is an open-source tool for visualizing LC-MS proteomics data from natural protein catabolism, demonstrating its ability to identify proteolytic cut sites in human and parasite systems.

The paper introduces MINNO, a tool that refines metabolic networks using empirical metabolomics data, demonstrating its application in studying non-model organisms like Borrelia species.