Florian Plaza Oñate

The paper identifies GBS CC17's competitive advantage over non-CC17 GBS in neonatal gut colonization through metagenomic analysis and in vitro experiments.

CroCoDeEL detects and quantifies cross-sample contamination in metagenomic data without negative controls or prior knowledge, showing high accuracy even at low contamination rates.

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

R package NeighborFinder infers a focal species' co-abundance neighbors via repeated cross-validated ℓ1 regression, reaching F1 ≥ 0.95 on simulated cohorts of 250 to 1000 samples.

This study examines how antibiotic treatment affects the gut phageome, finding reduced diversity and increased virulent phage blooms, which may help restore bacterial diversity through kill-the-winner dynamics.

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.

This study compares gut microbiota changes after LSG and LRYGB, finding LRYGB induces greater taxonomic and functional shifts than LSG.