Classical random Boolean networks (RBN) are not well suited to describe experimental data from time-course microarray, mainly because of the strict assumptions about the synchronicity of the regulatory mechanisms. In order to overcome this setback, a generalization of the RBN model is described and analyzed. Gene products (e.g., regulatory proteins) are introduced, with each one characterized by a specific decay time, thereby introducing a form of memory in the system. The dynamics of these networks is analyzed, and it is shown that the distribution of the decay times has a strong effect that can be adequately described and understood. The implications for the dynamical criticality of the networks are also discussed. © 2011, Mary Ann Liebert, Inc.

Graudenzi, A., Serra, R., Villani, M., Damiani, C., Colacci, A., Kauffman, S. (2011). Dynamical properties of a Boolean model of gene regulatory network with memory. JOURNAL OF COMPUTATIONAL BIOLOGY, 18(10), 1291-1303 [10.1089/cmb.2010.0069].

Dynamical properties of a Boolean model of gene regulatory network with memory

Graudenzi A
;
Serra R;Damiani C;
2011

Abstract

Classical random Boolean networks (RBN) are not well suited to describe experimental data from time-course microarray, mainly because of the strict assumptions about the synchronicity of the regulatory mechanisms. In order to overcome this setback, a generalization of the RBN model is described and analyzed. Gene products (e.g., regulatory proteins) are introduced, with each one characterized by a specific decay time, thereby introducing a form of memory in the system. The dynamics of these networks is analyzed, and it is shown that the distribution of the decay times has a strong effect that can be adequately described and understood. The implications for the dynamical criticality of the networks are also discussed. © 2011, Mary Ann Liebert, Inc.
Articolo in rivista - Articolo scientifico
criticality; gene regulatory networks; random Boolean networks; time-course microarray; timing; Computational Biology; Computer Simulation; Gene Expression Regulation; Time; Algorithms; Gene Regulatory Networks; Models, Genetic; Molecular Dynamics Simulation; Molecular Biology; Genetics; Computational Mathematics; Modeling and Simulation; Computational Theory and Mathematics
English
1291
1303
13
Graudenzi, A., Serra, R., Villani, M., Damiani, C., Colacci, A., Kauffman, S. (2011). Dynamical properties of a Boolean model of gene regulatory network with memory. JOURNAL OF COMPUTATIONAL BIOLOGY, 18(10), 1291-1303 [10.1089/cmb.2010.0069].
File in questo prodotto:
File Dimensione Formato  
jcb2011.pdf

Solo gestori archivio

Tipologia di allegato: Publisher’s Version (Version of Record, VoR)
Dimensione 390.2 kB
Formato Adobe PDF
390.2 kB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/60591
Citazioni
  • Scopus 49
  • ???jsp.display-item.citation.isi??? 41
Social impact