Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle Export

@article{citeulike:825694, abstract = {Motivation: To understand the behaviour of complex biological regulatory networks, a proper integration of molecular data into a full-fledge formal dynamical model is ultimately required. As most available data on regulatory interactions are qualitative, logical modelling offers an interesting framework to delineate the main dynamical properties of the underlying networks. Results: Transposing a generic model of the core network controlling the mammalian cell cycle into the logical framework, we compare different strategies to explore its dynamical properties. In particular, we assess the respective advantages and limits of synchronous versus asynchronous updating assumptions to delineate the asymptotical behaviour of regulatory networks. Furthermore, we propose several intermediate strategies to optimize the computation of asymptotical properties depending on available knowledge. Availability: The mammalian cell cycle model is available in a dedicated XML format (GINML) on our website, along with our logical simulation software GINsim (http://gin.univ-mrs.fr/GINsim). Higher resolution state transitions graphs are also found on this web site (Model Repository page). Contact: thieffry@ibdm.univ-mrs.fr 10.1093/bioinformatics/btl210}, address = {Institut de Biologie du D\'{e}veloppement de Marseille-Luminy, Campus scientifique de Luminy CNRS case 907, 13288 Marseille, France.}, author = {Faure, Adrien and Naldi, Aurelien and Chaouiya, Claudine and Thieffry, Denis}, citeulike-article-id = {825694}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btl210}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e124}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16873462}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16873462}, day = {15}, doi = {10.1093/bioinformatics/btl210}, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {boolean, cell-cycle, eukaryotes, mammals, modeling, network, regulation}, month = {July}, number = {14}, pages = {e124--131}, posted-at = {2008-11-18 14:20:36}, priority = {5}, title = {Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle}, url = {http://dx.doi.org/10.1093/bioinformatics/btl210}, volume = {22}, year = {2006} }

TY - JOUR ID - citeulike:825694 L3 - citeulike-article-id:825694 N2 - Motivation: To understand the behaviour of complex biological regulatory networks, a proper integration of molecular data into a full-fledge formal dynamical model is ultimately required. As most available data on regulatory interactions are qualitative, logical modelling offers an interesting framework to delineate the main dynamical properties of the underlying networks. Results: Transposing a generic model of the core network controlling the mammalian cell cycle into the logical framework, we compare different strategies to explore its dynamical properties. In particular, we assess the respective advantages and limits of synchronous versus asynchronous updating assumptions to delineate the asymptotical behaviour of regulatory networks. Furthermore, we propose several intermediate strategies to optimize the computation of asymptotical properties depending on available knowledge. Availability: The mammalian cell cycle model is available in a dedicated XML format (GINML) on our website, along with our logical simulation software GINsim (http://gin.univ-mrs.fr/GINsim). Higher resolution state transitions graphs are also found on this web site (Model Repository page). Contact: thieffry@ibdm.univ-mrs.fr 10.1093/bioinformatics/btl210 IS - 14 JF - Bioinformatics SN - 1460-2059 AD - Institut de Biologie du Développement de Marseille-Luminy, Campus scientifique de Luminy CNRS case 907, 13288 Marseille, France. EP - 131 TI - Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle VL - 22 SP - e124 KW - boolean KW - cell-cycle KW - eukaryotes KW - mammals KW - modeling KW - network KW - regulation AU - Faure, Adrien AU - Naldi, Aurelien AU - Chaouiya, Claudine AU - Thieffry, Denis PY - 2006/07/15/ UR - http://dx.doi.org/10.1093/bioinformatics/btl210 ER -