Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles. - Markus J. Herrgård; Stephen S. Fong; Bernhard Ø. Palsson (PLoS Comput. Biol., 2006)

Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation. - Christian L. Barrett; Markus J. Herrgård; Bernhard Ø. Palsson (BMC Syst. Biol., 2009)

Connecting extracellular metabolomic measurements to intracellular flux states in yeast. - Monica L. Mo; Bernhard Ø. Palsson; Markus J. Herrgård (BMC Syst. Biol., 2009)

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism. - Daniel Machado; Markus J. Herrgård (PLoS Comput. Biol., 2014)

Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction. - Daniel Machado; Markus J. Herrgård; Isabel Rocha (PLoS Comput. Biol., 2016)

MARSI: metabolite analogues for rational strain improvement. - João G. R. Cardoso; Ahmad A. Zeidan; Kristian Jensen; Nikolaus Sonnenschein; Ana Rute Neves; Markus J. Herrgård (Bioinform., 2018)

Microbial community dynamics revisited. - Boyang Ji; Markus J. Herrgård; Jens Nielsen (Nat. Comput. Sci., 2021)