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 |
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Keywords
- Boolean networks
- Constraint-based modeling
- Flux balance analysis
- MILP
- Metabolic modeling
- Mixed-integer programming
- Transcriptional regulation
ASJC Scopus subject areas
- Molecular Biology
- Genetics
Cite this
Coupling fluxes, enzymes, and regulation in genome-scale metabolic models. / Jensen, Paul A.
Methods in Molecular Biology. Humana Press Inc., 2018. p. 337-351 (Methods in Molecular Biology; Vol. 1716).Research output: Chapter in Book/Report/Conference proceeding › Chapter
}
TY - CHAP
T1 - Coupling fluxes, enzymes, and regulation in genome-scale metabolic models
AU - Jensen, Paul A
PY - 2018/1/1
Y1 - 2018/1/1
N2 - 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.
AB - 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.
KW - Boolean networks
KW - Constraint-based modeling
KW - Flux balance analysis
KW - MILP
KW - Metabolic modeling
KW - Mixed-integer programming
KW - Transcriptional regulation
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UR - http://www.scopus.com/inward/citedby.url?scp=85037688645&partnerID=8YFLogxK
U2 - 10.1007/978-1-4939-7528-0_15
DO - 10.1007/978-1-4939-7528-0_15
M3 - Chapter
C2 - 29222761
AN - SCOPUS:85037688645
T3 - Methods in Molecular Biology
SP - 337
EP - 351
BT - Methods in Molecular Biology
PB - Humana Press Inc.
ER -