José P. Faria

The ModelSEED Biochemistry Database, 2026 update: grading multi-source thermodynamics

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

Data coherence over data volume drives generalisable genome-based prediction of microbial carbon utilisation

This study shows that filtering genomes based on coherent genotype-phenotype relationships improves cross-dataset prediction of microbial carbon utilisation, outperforming larger but less coherent datasets.

Integrative Modeling and Analysis of Fungal Central Carbon Metabolism

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

Emergence and disruption of cooperativity in a denitrifying microbial community

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: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction

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

kb_DRAM: Annotating and functional profiling of genomes with DRAM in KBase

kb_DRAM integrates DRAM tools into KBase for microbial and viral genome annotation and metabolic modeling through a user-friendly interface.

TranSyT, an innovative framework for identifying transport systems

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

The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi, and microbes

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: A community-driven effort towards a standardized genome-scale metabolic model test suite

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.

The DOE Systems Biology Knowledgebase (KBase)

Open-source KBase platform unites reference genomes and biochemistry, over 70 apps, Jupyter-based Narratives with provenance, and a Docker SDK for reproducible plant and microbial systems biology.