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.
| Original language | English (US) |
|---|---|
| Title of host publication | Methods in Molecular Biology |
| Publisher | Humana Press Inc. |
| Pages | 337-351 |
| Number of pages | 15 |
| DOIs | |
| State | Published - Jan 1 2018 |
Publication series
| Name | Methods in Molecular Biology |
|---|---|
| Volume | 1716 |
| ISSN (Print) | 1064-3745 |
Keywords
- 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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Cite this
Jensen, P. A. (2018). Coupling fluxes, enzymes, and regulation in genome-scale metabolic models. In Methods in Molecular Biology (pp. 337-351). (Methods in Molecular Biology; Vol. 1716). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7528-0_15