@inbook{a101b2798400468999568095677ad585,
title = "Coupling fluxes, enzymes, and regulation in genome-scale metabolic models",
abstract = "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.",
keywords = "Boolean networks, Constraint-based modeling, Flux balance analysis, MILP, Metabolic modeling, Mixed-integer programming, Transcriptional regulation",
author = "Jensen, {Paul A.}",
year = "2018",
month = jan,
day = "1",
doi = "10.1007/978-1-4939-7528-0_15",
language = "English (US)",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "337--351",
booktitle = "Methods in Molecular Biology",
}