Attractor computation using interconnected Boolean networks: testing growth rate models in E. Coli

Madalena Chaves 1 Alfonso Carta 1
1 BIOCORE - Biological control of artificial ecosystems
LOV - Laboratoire d'océanographie de Villefranche, CRISAM - Inria Sophia Antipolis - Méditerranée , INRA - Institut National de la Recherche Agronomique
Abstract : Boolean networks provide a useful tool to address questions on the structure of large biochemical interactions since they do not require kinetic details and, in addition, a wide range of computational tools and algorithms is available to exactly compute and study the dynamical properties of these models. A recently developed method has shown that the attractors, or asymptotic behavior, of an asynchronous Boolean network can be computed at a much lower cost if the network is written as an interconnection of two smaller modules. We have applied this methodology to study the interconnection of two Boolean models to explore bacterial growth and its interactions with the cellular gene expression machinery, with a focus on growth dynamics as a function of ribosomes, RNA polymerase and other "bulk" proteins inside the cell. The discrete framework permits easier testing of different combinations of biochemical interactions, leading to hypotheses elimination and model discrimination, and thus providing useful insights for the construction of a more detailed dynamical growth model.
Type de document :
Article dans une revue
Theoretical Computer Science, Elsevier, 2014, pp.17. 〈10.1016/j.tcs.2014.06.021〉
Liste complète des métadonnées

Littérature citée [30 références]  Voir  Masquer  Télécharger

https://hal.inria.fr/hal-01095196
Contributeur : Jean-Luc Gouzé <>
Soumis le : lundi 15 décembre 2014 - 11:35:00
Dernière modification le : mardi 17 avril 2018 - 11:48:04
Document(s) archivé(s) le : lundi 16 mars 2015 - 11:10:39

Fichier

ecoli-bool-web-version-final.p...
Fichiers produits par l'(les) auteur(s)

Identifiants

Collections

Citation

Madalena Chaves, Alfonso Carta. Attractor computation using interconnected Boolean networks: testing growth rate models in E. Coli. Theoretical Computer Science, Elsevier, 2014, pp.17. 〈10.1016/j.tcs.2014.06.021〉. 〈hal-01095196〉

Partager

Métriques

Consultations de la notice

268

Téléchargements de fichiers

139