Damien Eveillard

Satellite-gene abundance fusion reveals global hotspots of ocean ecosystem services

The paper identifies global hotspots of plankton-based ecosystem services by integrating satellite data with metagenomic functions and machine learning.

MIMEco: Multi-objective metabolic modeling to predict and explain pairwise interactions

MIMEco predicts pairwise microbial interactions using multi-objective metabolic modeling without requiring abundance data, validated by replicating experimental results with Escherichia coli.

HUMESS: Integrating Quantitative Transcriptomic Analysis and Metabolic Modeling to Unveil Condition-Specific Gene Signatures

HUMESS integrates transcriptomic data with metabolic modeling to identify condition-specific gene signatures by prioritizing genes based on metabolic significance.

Planetary-scale heterotrophic microbial community modeling assesses metabolic synergy and viral impacts

The paper develops a genome-scale metabolic model for ocean microbial communities to infer metabolic processes and viral impacts on biogeochemical cycles.

Community metabolic modeling of host-microbiota interactions through multi-objective optimization

This paper models host-microbiota interactions using in silico metabolic models and multi-objective optimization to predict microbial interaction types and quantify their effects on epithelial cell maintenance.

Towards modeling genome-scale knowledge in the global ocean

The paper integrates a genome-scale model into an Earth System Model to study how environmental gradients affect metabolic processes in marine cyanobacteria.

Unveiling abundance-dependent metabolic phenotypes of microbial communities

The paper introduces a method to explore abundance-growth space for microbial communities, revealing abundance-dependent metabolic phenotypes through constraint-based modeling.

Bringing large scale top-down metabolic modelling to eukaryotes with PhotoEukStein: a meta-model for unicellular phototrophs

The paper introduces PhotoEukStein, a meta-model for unicellular phototrophic eukaryotes, enabling automated derivation of genome-scale metabolic models from genomes to predict functional traits.

Impact of the species compartment definition on quantitative modeling of microbial communities

This paper compares the impact of using single vs. multiple compartments in microbial community modeling using flux module analysis on two microbial systems.