Canalization and control in automata networks: body segmentation in  Drosophila melanogaster

Marques-Pita, Manuel; Rocha, Luís M.

Publication

Canalization and control in automata networks: body segmentation in Drosophila melanogaster

2013-03-08Journal article

dc.contributor.author	Marques-Pita, Manuel
dc.contributor.author	Rocha, Luís M.
dc.date.accessioned	2015-11-02T15:53:37Z
dc.date.available	2015-11-02T15:53:37Z
dc.date.issued	2013-03-08
dc.description.abstract	We present schema redescription as a methodology to characterize canalization in automata networks used to model biochemical regulation and signalling. In our formulation, canalization becomes synonymous with redundancy present in the logic of automata. This results in straightforward measures to quantify canalization in an automaton (micro-level), which is in turn integrated into a highly scalable framework to characterize the collective dynamics of large-scale automata networks (macro-level). This way, our approach provides a method to link micro- to macro-level dynamics -- a crux of complexity. Several new results ensue from this methodology: uncovering of dynamical modularity (modules in the dynamics rather than in the structure of networks), identification of minimal conditions and critical nodes to control the convergence to attractors, simulation of dynamical behaviour from incomplete information about initial conditions, and measures of macro-level canalization and robustness to perturbations. We exemplify our methodology with a well-known model of the intra- and inter cellular genetic regulation of body segmentation in Drosophila melanogaster. We use this model to show that our analysis does not contradict any previous findings. But we also obtain new knowledge about its behaviour: a better understanding of the size of its wild-type attractor basin (larger than previously thought), the identification of novel minimal conditions and critical nodes that control wild-type behaviour, and the resilience of these to stochastic interventions. Our methodology is applicable to any complex network that can be modelled using automata, but we focus on biochemical regulation and signalling, towards a better understanding of the (decentralized) control that orchestrates cellular activity -- with the ultimate goal of explaining how do cells and tissues 'compute'.	pt_PT
dc.identifier	10.1371/journal.pone.0055946
dc.identifier.citation	Marques-Pita M, Rocha LM (2013) Canalization and Control in Automata Networks: Body Segmentation in Drosophila melanogaster . PLoS ONE 8(3): e55946. doi:10.1371/journal.pone.0055946	pt_PT
dc.identifier.doi	10.1371/journal.pone.0055946
dc.identifier.uri	http://hdl.handle.net/10400.7/458
dc.language.iso	eng	pt_PT
dc.peerreviewed	yes	pt_PT
dc.publisher	PLOS	pt_PT
dc.relation	Collective Computation and Control in Complex Biochemical Systems
dc.relation.publisherversion	http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0055946	pt_PT
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	pt_PT
dc.subject	Body Patterning	pt_PT
dc.subject	Drosophila melanogaster	pt_PT
dc.subject	Models, Biological	pt_PT
dc.title	Canalization and control in automata networks: body segmentation in Drosophila melanogaster	pt_PT
dc.type	journal article
dspace.entity.type	Publication
oaire.awardTitle	Collective Computation and Control in Complex Biochemical Systems
oaire.awardURI	info:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FEIA-CCO%2F114108%2F2009/PT
oaire.citation.endPage	34	pt_PT
oaire.citation.issue	3	pt_PT
oaire.citation.startPage	1	pt_PT
oaire.citation.title	PLOS One	pt_PT
oaire.citation.volume	8	pt_PT
oaire.fundingStream	3599-PPCDT
project.funder.identifier	http://doi.org/10.13039/501100001871
project.funder.name	Fundação para a Ciência e a Tecnologia
rcaap.rights	openAccess	pt_PT
rcaap.type	article	pt_PT
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