Filipe Liu

The paper updates the ModelSEED Biochemistry Database with expanded compounds and reactions, integrating multi-source thermodynamic data and grading reaction reliability.

The paper integrates thirteen fungal metabolic models into a unified framework, improves their consistency, and uses them to analyze bioenergetic differences across species.

This study identifies pathway partitioning as a mechanism for complete denitrification in microbial communities and shows how imbalances in substrate utilization can disrupt cooperativity and lead to nitrous oxide emissions.

ModelSEED v2 improves genome-scale metabolic model reconstruction with enhanced energy metabolism and better pathway curation, leading to more accurate and comprehensive models.

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

The paper introduces the ModelSEED biochemistry database, which integrates metabolic annotations and supports the reconstruction and analysis of metabolic models for plants, fungi, and microbes.

Memote, open-source Python software, runs a community-maintained, partly scored test suite (consistency, biomass, annotations, optional experimental data) on SBML-encoded genome-scale metabolic models, once or through continuous integration.