Thomas J. Moutinho

Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions

The paper introduces a method to quantify genomic, biochemical, and phenotypic evidence for metabolic network reconstructions, improving accuracy by integrating continuous evidence.

Medusa: software to build and analyze ensembles of genome-scale metabolic network reconstructions

Medusa is a Python package that generates and analyzes ensembles of genome-scale metabolic network reconstructions, enabling ensemble simulations and machine learning-guided curation.

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

RIPTiDe improves metabolic predictions by integrating transcriptomic data with flux minimization to identify cost-effective metabolic pathways in bacteria without requiring knowledge of growth conditions.

Functional Anabolic Network Analysis of Human-associated Lactobacillus Strains

This study introduces PROTEAN, a method to analyze metabolic capabilities of Lactobacillus strains, revealing site-specific differences in predicted metabolic production.