A perturbation approach for refining Boolean models of cell cycle regulation

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dc.contributor.authorBanerjee, Ananden
dc.contributor.authorRahaman, Asif Iqbalen
dc.contributor.authorMehandale, Aloken
dc.contributor.authorKraikivski, Pavelen
dc.date.accessioned2025-01-02T18:52:07Zen
dc.date.available2025-01-02T18:52:07Zen
dc.date.issued2024-09-06en
dc.description.abstractConsiderable effort is required to build mathematical models of large protein regulatory networks. Utilizing computational algorithms that guide model development can significantly streamline the process and enhance the reliability of the resulting models. In this article, we present a perturbation approach for developing data-centric Boolean models of cell cycle regulation. To evaluate networks, we assign a score based on their steady states and the dynamical trajectories corresponding to the initial conditions. Then, perturbation analysis is used to find new networks with lower scores, in which dynamical trajectories traverse through the correct cell cycle path with high frequency. We apply this method to refine Boolean models of cell cycle regulation in budding yeast and mammalian cells.en
dc.description.versionPublished versionen
dc.format.extent14 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifierARTN e0306523 (Article number)en
dc.identifier.doihttps://doi.org/10.1371/journal.pone.0306523en
dc.identifier.eissn1932-6203en
dc.identifier.issn1932-6203en
dc.identifier.issue9en
dc.identifier.orcidKraikivski, Pavel [0000-0001-7742-0140]en
dc.identifier.otherPONE-D-23-41629 (PII)en
dc.identifier.pmid39240895en
dc.identifier.urihttps://hdl.handle.net/10919/123872en
dc.identifier.volume19en
dc.language.isoenen
dc.publisherPLOSen
dc.relation.urihttps://www.ncbi.nlm.nih.gov/pubmed/39240895en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subject.meshAnimalsen
dc.subject.meshHumansen
dc.subject.meshSaccharomycetalesen
dc.subject.meshSaccharomyces cerevisiaeen
dc.subject.meshCell Cycleen
dc.subject.meshAlgorithmsen
dc.subject.meshModels, Biologicalen
dc.subject.meshGene Regulatory Networksen
dc.titleA perturbation approach for refining Boolean models of cell cycle regulationen
dc.title.serialPLOS Oneen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherJournalen
dcterms.dateAccepted2024-06-19en
pubs.organisational-groupVirginia Techen
pubs.organisational-groupVirginia Tech/Scienceen
pubs.organisational-groupVirginia Tech/Science/Dean of Scienceen

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