Markus J. Herrgård

The paper describes an automated workflow for generating high-throughput microbial multi-omics datasets and evaluates its effectiveness with three model organisms.

SmartPeak automates metabolomics data processing with algorithms for alignment, calibration, and peak integration, improving reproducibility and throughput.

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.

This study benchmarks kinetic models of Escherichia coli metabolism to evaluate their performance in predicting metabolic fluxes under genetic and environmental perturbations.

The paper reconstructs and validates a genome-scale metabolic model for Lactobacillus reuteri JCM 1112T, demonstrating its accuracy in predicting metabolic behavior and identifying strategies for metabolic engineering.

The paper presents a genome-scale metabolic model for Methylococcus capsulatus, showing that methane oxidation by pMMO is driven by uphill electron transfer with reduced efficiency.