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A Model of Yeast Cell-Cycle Regulation Based on a Standard Component Modeling Strategy for Protein Regulatory Networks

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dc.contributor.authorLaomettachit, Teeraphanen
dc.contributor.authorChen, Katherine C.en
dc.contributor.authorBaumann, William T.en
dc.contributor.authorTyson, John J.en
dc.contributor.departmentElectrical and Computer Engineeringen
dc.contributor.departmentBiological Sciencesen
dc.date.accessioned2016-12-09T21:42:50Zen
dc.date.available2016-12-09T21:42:50Zen
dc.date.issued2016-05-17en
dc.description.abstractTo understand the molecular mechanisms that regulate cell cycle progression in eukaryotes, a variety of mathematical modeling approaches have been employed, ranging from Boolean networks and differential equations to stochastic simulations. Each approach has its own characteristic strengths and weaknesses. In this paper, we propose a “standard component” modeling strategy that combines advantageous features of Boolean networks, differential equations and stochastic simulations in a framework that acknowledges the typical sorts of reactions found in protein regulatory networks. Applying this strategy to a comprehensive mechanism of the budding yeast cell cycle, we illustrate the potential value of standard component modeling. The deterministic version of our model reproduces the phenotypic properties of wild-type cells and of 125 mutant strains. The stochastic version of our model reproduces the cell-to-cell variability of wild-type cells and the partial viability of the CLB2-dbΔ clb5Δ mutant strain. Our simulations show that mathematical modeling with “standard components” can capture in quantitative detail many essential properties of cell cycle control in budding yeast.en
dc.description.versionPublished versionen
dc.format.extent43 pagesen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1371/journal.pone.0153738en
dc.identifier.issn1932-6203en
dc.identifier.issue5en
dc.identifier.urihttp://hdl.handle.net/10919/73645en
dc.identifier.volume11en
dc.language.isoenen
dc.publisherPLOSen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000376282300005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectkinase inhibitor p40(sic1)en
dc.subjectbudding-yeasten
dc.subjectsaccharomyces-cerevisiaeen
dc.subjectmitotic exiten
dc.subjectphosphatase cdc14en
dc.subjectmultisite phosphorylationen
dc.subjectmathematical-modelen
dc.subjectgene-expressionen
dc.subjectrepressor whi5en
dc.subjectpolo kinaseen
dc.titleA Model of Yeast Cell-Cycle Regulation Based on a Standard Component Modeling Strategy for Protein Regulatory Networksen
dc.title.serialPLOS ONEen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Faculty of Health Sciencesen
pubs.organisational-group/Virginia Tech/Scienceen
pubs.organisational-group/Virginia Tech/Science/Biological Sciencesen
pubs.organisational-group/Virginia Tech/Science/COS T&R Facultyen
pubs.organisational-group/Virginia Tech/University Distinguished Professorsen

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