Titre
Synchronous versus asynchronous modeling of gene regulatory networks.
Type
article
Institution
UNIL/CHUV/Unisanté + institutions partenaires
Périodique
Auteur(s)
Garg, A.
Auteure/Auteur
Di Cara, A.
Auteure/Auteur
Xenarios, I.
Auteure/Auteur
Mendoza, L.
Auteure/Auteur
De Micheli, G.
Auteure/Auteur
Liens vers les personnes
Liens vers les unités
ISSN
1367-4811
Statut éditorial
Publié
Date de publication
2008
Volume
24
Numéro
17
Première page
1917
Dernière page/numéro d’article
1925
Langue
anglais
Résumé
MOTIVATION: In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems. This has been further facilitated by the increasing availability of experimental data on gene-gene, protein-protein and gene-protein interactions. The two dynamical properties that are often experimentally testable are perturbations and stable steady states. Although a lot of work has been done on the identification of steady states, not much work has been reported on in silico modeling of cellular differentiation processes.
RESULTS: In this manuscript, we provide algorithms based on reduced ordered binary decision diagrams (ROBDDs) for Boolean modeling of gene regulatory networks. Algorithms for synchronous and asynchronous transition models have been proposed and their corresponding computational properties have been analyzed. These algorithms allow users to compute cyclic attractors of large networks that are currently not feasible using existing software. Hereby we provide a framework to analyze the effect of multiple gene perturbation protocols, and their effect on cell differentiation processes. These algorithms were validated on the T-helper model showing the correct steady state identification and Th1-Th2 cellular differentiation process.
AVAILABILITY: The software binaries for Windows and Linux platforms can be downloaded from http://si2.epfl.ch/~garg/genysis.html.
RESULTS: In this manuscript, we provide algorithms based on reduced ordered binary decision diagrams (ROBDDs) for Boolean modeling of gene regulatory networks. Algorithms for synchronous and asynchronous transition models have been proposed and their corresponding computational properties have been analyzed. These algorithms allow users to compute cyclic attractors of large networks that are currently not feasible using existing software. Hereby we provide a framework to analyze the effect of multiple gene perturbation protocols, and their effect on cell differentiation processes. These algorithms were validated on the T-helper model showing the correct steady state identification and Th1-Th2 cellular differentiation process.
AVAILABILITY: The software binaries for Windows and Linux platforms can be downloaded from http://si2.epfl.ch/~garg/genysis.html.
PID Serval
serval:BIB_2182CDF3CDC9
PMID
Open Access
Oui
Date de création
2012-10-18T07:13:53.076Z
Date de création dans IRIS
2025-05-20T15:50:14Z
Fichier(s)![Vignette d'image]()
En cours de chargement...
Nom
18614585_BIB_2182CDF3CDC9.pdf
Version du manuscrit
published
Taille
222.89 KB
Format
Adobe PDF
PID Serval
serval:BIB_2182CDF3CDC9.P001
URN
urn:nbn:ch:serval-BIB_2182CDF3CDC92
Somme de contrôle
(MD5):85e1513f2c3de9fc44ba257a3f1aa64b