Arianna Basile

CarveMe-GutMicrobes reconstructs genome-scale metabolic models for gut microbes from genomic data, showing high accuracy in predicting gene essentiality and metabolite secretion.

This study examines how bacterial proteomes and metabolomes change in response to interspecies interactions in gut microbiota co-cultures, revealing extensive molecular reorganization and emergent metabolic pathways.

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

The paper introduces FROG analysis to standardize reproducibility assessments of genome-scale metabolic models, resulting in full reproducibility of all tested models.

The paper identifies key microbial interactions and metabolic pathways that confer resistance to C. difficile invasion using synthetic and clinical communities.

This study uses longitudinal flux balance analysis of a Crohn's disease patient's microbiome to identify time-correlated metabolic alterations and their systemic effects.

NEMETEX visualizes metabolic exchange networks from metagenomics and flux balance analysis data, integrating abundance, taxonomy, and exchange rates for easier interpretation.