Emanuel Cunha

The paper presents the first curated genome-scale metabolic model for L. rhamnosus GG, validated using multiple approaches and provides insights into its nutrient requirements and secretions.

The paper introduces FROG analysis to standardize reproducibility assessments of genome-scale metabolic models, resulting in full reproducibility of all tested models.

The paper updates a genome-scale metabolic model for Xylella fastidiosa subsp. pauca, validating it against experimental data for aerobic metabolism and gum production.

merlin v4.0 improves genome-scale metabolic model reconstruction with new algorithms and tools, supporting multiple organisms and offering competitive performance.

TranSyT automates the integration of transport reactions into genome-scale metabolic models by compiling curated transporter data and providing rapid genome annotation.

This paper develops the first multi-tissue diel genome-scale metabolic model for Quercus suber, highlighting suberin biosynthesis pathways and enabling analysis of tissue interactions.