Filippo Martinelli

StereoMapper: Clarifying Metabolite Identity Through Stereochemically Aware Relationship Assignment

StereoMapper clarifies metabolite identity by assigning stereochemically aware relationships, achieving high performance in benchmark datasets and improving GEM accuracy.

Elucidating a potential role of the infant gut microbiome on the bioavailability of L-tyrosine in phenylketonuria

The paper uses metabolic models to show that gut microbiome composition affects L-tyrosine availability in PKU, suggesting microbiome-targeted therapies.

The MicroMap is a network visualisation resource for microbiome metabolism

The paper introduces the MicroMap, a curated metabolic network visualization resource for microbiome metabolism, integrating with existing tools and providing educational and comparative capabilities.

APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites

APOLLO provides 247,092 genome-scale metabolic models of human microbes, enabling strain-level taxonomic prediction and disease-associated metabolite analysis.

Integration of constraint-based modeling with fecal metabolomics reveals large deleterious effects of Fusobacteria species on community butyrate production

This study integrates constraint-based community modeling with fecal metabolomics to show Fusobacteria negatively impact butyrate production in gut microbiomes.

AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities.

AGORA2 reconstructs the human microbiome at scale, revealing individual-specific drug metabolism capabilities and correlations with clinical parameters.