ToyLIFE: a computational framework to study the multi-level organisation of the genotype-phenotype map

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dc.contributor.author Fernández Arias, Clemente
dc.contributor.author Catalán Fernández, Pablo
dc.contributor.author Manrubia, Susanna C.
dc.contributor.author Cuesta, José A.
dc.date.accessioned 2015-07-20T10:07:53Z
dc.date.available 2015-07-20T10:07:53Z
dc.date.issued 2014-12
dc.identifier.bibliographicCitation Scientific Reports 4, 7549 (2014), pp. 1-19
dc.identifier.issn 2045-2322
dc.identifier.uri http://hdl.handle.net/10016/21429
dc.description.abstract The genotype-phenotype map is an essential object to understand organismal complexity and adaptability. However, its experimental characterisation is a daunting task. Thus, simple models have been proposed and investigated. They have revealed that genotypes differ in their robustness to mutations; phenotypes are represented by a broadly varying number of genotypes, and simple point mutations suffice to navigate the space of genotypes while maintaining a phenotype. Nonetheless, most current models focus only on one level of the map (folded molecules, gene regulatory networks, or networks of metabolic reactions), so that many relevant questions cannot be addressed. Here we introduce toyLIFE, a multi-level model for the genotype-phenotype map based on simple genomes and interaction rules from which a complex behaviour at upper levels emerges - remarkably plastic gene regulatory networks and metabolism. toyLIFE is a tool that permits the investigation of how different levels are coupled, in particular how and where mutations affect phenotype or how the presence of certain metabolites determines the dynamics of toyLIFE gene regulatory networks. The model can easily incorporate evolution through more complex mutations, recombination, or gene duplication and deletion, thus opening an avenue to explore extended genotype-phenotype maps.
dc.description.sponsorship This work was supported through projects FIS2011-22449 (CFA, PC and JAC) and FIS2011{27569 (SM) of the Spanish MINECO.
dc.format.extent 20
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Macmillan
dc.rights © 2014 Macmillan
dc.rights Atribución-NoComercial-CompartirIgual 3.0 España
dc.rights.uri http://creativecommons.org/licenses/by-nc-sa/3.0/es/
dc.subject.other Computational models
dc.subject.other Evolutionary theory
dc.subject.other Regulatory networks
dc.subject.other Evolvability
dc.title ToyLIFE: a computational framework to study the multi-level organisation of the genotype-phenotype map
dc.type article
dc.description.status Publicado
dc.relation.publisherversion http://dx.doi.org/10.1038/srep07549
dc.subject.eciencia Matemáticas
dc.identifier.doi 10.1038/srep07549
dc.rights.accessRights openAccess
dc.relation.projectID Gobierno de España. FIS2011-22449/PRODIEVO
dc.relation.projectID Gobierno de España. FIS2011–27569
dc.type.version publishedVersion
dc.identifier.publicationfirstpage 1
dc.identifier.publicationlastpage 19
dc.identifier.publicationtitle Scientific Reports
dc.identifier.publicationvolume 4-4549
dc.identifier.uxxi AR/0000016025
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