Dynamic elementary mode modelling of non-steady state flux data

Abel Folch-Fortuny*, Bas Teusink, Huub C.J. Hoefsloot, Age K. Smilde, Alberto Ferrer

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review


Background: A novel framework is proposed to analyse metabolic fluxes in non-steady state conditions, based on the new concept of dynamic elementary mode (dynEM): an elementary mode activated partially depending on the time point of the experiment. Results: Two methods are introduced here: dynamic elementary mode analysis (dynEMA) and dynamic elementary mode regression discriminant analysis (dynEMR-DA). The former is an extension of the recently proposed principal elementary mode analysis (PEMA) method from steady state to non-steady state scenarios. The latter is a discriminant model that permits to identify which dynEMs behave strongly different depending on the experimental conditions. Two case studies of Saccharomyces cerevisiae, with fluxes derived from simulated and real concentration data sets, are presented to highlight the benefits of this dynamic modelling. Conclusions: This methodology permits to analyse metabolic fluxes at early stages with the aim of i) creating reduced dynamic models of flux data, ii) combining many experiments in a single biologically meaningful model, and iii) identifying the metabolic pathways that drive the organism from one state to another when changing the environmental conditions.

Original languageEnglish
Article number71
Pages (from-to)1-15
Number of pages15
JournalBMC Systems Biology
Publication statusPublished - 18 Jun 2018


  • Cross validation
  • Dynamic modelling
  • Elementary mode
  • Metabolic network
  • N-way
  • Partial least squares regression discriminant analysis
  • Principal component analysis
  • Principal elementary mode analysis


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