Robert W. Cottingham

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.

KBase Research Agent: Automated Multi-Agent Workflow Construction for Reproducible Genome Analysis

The KBase Research Agent automates genome analysis workflows, producing reproducible results and annotated genomes without human intervention.

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.

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.

Dissecting Complexity: The Hidden Impact of Application Parameters on Bioinformatics Research

This paper examines the impact of application parameters on bioinformatics tools and proposes a methodology to systematically explore these parameters across different tools and scientific inquiries.

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.

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.