Clémence Frioux

This study combines HiFi long-read and short-read sequencing to improve MAG recovery and binning accuracy in soil microbiomes.

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

The paper integrates metagenome-scale metabolic modeling and metabolomics to analyze Microcystis phycospheres, revealing metabolic interactions and functional differences among strains.

MetaNetMap automates mapping of metabolomic annotations onto genome-scale metabolic networks through direct, conversion-table-bridged and partial identifier matching, reproducing 311 mappings from a Parkinson's disease study.

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.

The paper develops a computational framework to model soil microbiome metabolic potential in the Atacama Desert, identifying key species and functions across different environmental conditions.

Seed2LP predicts nutritional requirements (seeds) for microorganisms using hybrid metabolic modeling, improving seed inference over graph-based methods in genome-scale metabolic networks.

Mapler evaluates Hi-Fi long read metagenome assemblies, providing metrics to assess quality and identify bottlenecks in genome reconstruction.

AuCoMe reduces technical biases in metabolic network comparisons across diverse genomes and identifies shared and divergent metabolic traits.

This paper models the metabolism of a three-species bacterial community during cheese production using genome-scale models and omics data integration, accurately predicting community dynamics and interactions.

EsMeCaTa estimates consensus proteomes and metabolic functions from taxonomic data, validated on environmental datasets and applied to a methanogenic reactor study.

Metage2Metabo identifies keystone species in large microbiotas by analyzing metabolic networks and complementarity.

This paper presents the genome and metabolic network of Ectocarpus subulatus, a stress-tolerant brown alga, and identifies features contributing to its stress tolerance.

The paper identifies metabolic complementarities between a brown alga and its associated bacteria, showing that selected bacterial consortia enhance algal growth and metabolite exchange.