2.50
HDL Handle:
http://hdl.handle.net/10033/189005
Title:
From binary to multivalued to continuous models: the lac operon as a case study.
Authors:
Franke, Raimo; Theis, Fabian J; Klamt, Steffen
Abstract:
Using the lac operon as a paradigmatic example for a gene regulatory system in prokaryotes, we demonstrate how qualitative knowledge can be initially captured using simple discrete (Boolean) models and then stepwise refined to multivalued logical models and finally to continuous (ODE) models. At all stages, signal transduction and transcriptional regulation is integrated in the model description. We first show the potential benefit of a discrete binary approach and discuss then problems and limitations due to indeterminacy arising in cyclic networks. These limitations can be partially circumvented by using multilevel logic as generalization of the Boolean framework enabling one to formulate a more realistic model of the lac operon. Ultimately a dynamic description is needed to fully appreciate the potential dynamic behavior that can be induced by regulatory feedback loops. As a very promising method we show how the use of multivariate polynomial interpolation allows transformation of the logical network into a system of ordinary differential equations (ODEs), which then enables the analysis of key features of the dynamic behavior.
Affiliation:
Department of Chemical Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany. raimo.franke@helmholtz-hzi.de
Citation:
From binary to multivalued to continuous models: the lac operon as a case study. 2010, 7 (1): J Integr Bioinform
Journal:
Journal of integrative bioinformatics
Issue Date:
2010
URI:
http://hdl.handle.net/10033/189005
DOI:
10.2390/biecoll-jib-2010-151
PubMed ID:
21200084
Type:
Article
Language:
en
ISSN:
1613-4516
Appears in Collections:
Publications of Dept. Chemical Biology (CBIO)

Full metadata record

DC FieldValueLanguage
dc.contributor.authorFranke, Raimoen
dc.contributor.authorTheis, Fabian Jen
dc.contributor.authorKlamt, Steffenen
dc.date.accessioned2011-11-08T09:37:52Z-
dc.date.available2011-11-08T09:37:52Z-
dc.date.issued2010-
dc.identifier.citationFrom binary to multivalued to continuous models: the lac operon as a case study. 2010, 7 (1): J Integr Bioinformen
dc.identifier.issn1613-4516-
dc.identifier.pmid21200084-
dc.identifier.doi10.2390/biecoll-jib-2010-151-
dc.identifier.urihttp://hdl.handle.net/10033/189005-
dc.description.abstractUsing the lac operon as a paradigmatic example for a gene regulatory system in prokaryotes, we demonstrate how qualitative knowledge can be initially captured using simple discrete (Boolean) models and then stepwise refined to multivalued logical models and finally to continuous (ODE) models. At all stages, signal transduction and transcriptional regulation is integrated in the model description. We first show the potential benefit of a discrete binary approach and discuss then problems and limitations due to indeterminacy arising in cyclic networks. These limitations can be partially circumvented by using multilevel logic as generalization of the Boolean framework enabling one to formulate a more realistic model of the lac operon. Ultimately a dynamic description is needed to fully appreciate the potential dynamic behavior that can be induced by regulatory feedback loops. As a very promising method we show how the use of multivariate polynomial interpolation allows transformation of the logical network into a system of ordinary differential equations (ODEs), which then enables the analysis of key features of the dynamic behavior.en
dc.language.isoenen
dc.subject.meshAlgorithmsen
dc.subject.meshComputer Simulationen
dc.subject.meshGenes, Regulatoren
dc.subject.meshLac Operonen
dc.titleFrom binary to multivalued to continuous models: the lac operon as a case study.en
dc.typeArticleen
dc.contributor.departmentDepartment of Chemical Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany. raimo.franke@helmholtz-hzi.deen
dc.identifier.journalJournal of integrative bioinformaticsen

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