Coupling fluxes, enzymes, and regulation in genome-scale metabolic models

Research output: Chapter in Book/Report/Conference proceedingChapter


Genome-scale models have expanded beyond their metabolic origins. Multiple modeling frameworks are required to combine metabolism with enzymatic networks, transcription, translation, and regulation. Mathematical programming offers a powerful set of tools for tackling these “multi-modality” models, although special attention must be paid to the connections between modeling types. This chapter reviews common methods for combining metabolic and discrete logical models into a single mathematical programming framework. Best practices, caveats, and recommendations are presented for the most commonly used software packages. Methods for troubleshooting large sets of logical rules are also discussed.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages15
StatePublished - Jan 1 2018

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Boolean networks
  • Constraint-based modeling
  • Flux balance analysis
  • MILP
  • Metabolic modeling
  • Mixed-integer programming
  • Transcriptional regulation

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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