Mathieu Almeida

The paper uses the enterosignature model to stratify gut microbiome variation and links functional metabolic patterns to host health outcomes across multiple cohorts.

This study investigates whether GBA1 heterozygosity affects gut microbiome composition in a mouse model, finding no significant differences between genotypes.

The paper develops and evaluates optimized computational and experimental methods for analyzing the human mycobiome, identifying novel fungal species in oral and gut samples.

StrainFLAIR uses variation graphs to estimate strain-level abundances in metagenomic samples, showing effectiveness on both simulated and real datasets.

The paper introduces the reactobiome, a stratification method for the human gut microbiome, identifying five reactotypes with distinct metabolic features and validating them in a longitudinal cohort.

MSPminer reconstitutes microbial pan-genomes from shotgun metagenomic data by binning co-abundant genes, improving sensitivity over existing tools.

MetaCompass improves metagenomic assembly by combining reference-guided and de novo methods, enhancing completeness and accuracy over existing approaches.