アブストラクト
| Date | May 7, 2007 |
| Speaker | Dr. Denis Thieffry, Universitee de la Mediterranee, Marseille, France |
| Title | Logical modelling of genetic regulatory networks |
| Abstract | To understand the behaviour of the complex regulatory network
controlling the mammalian cell cycle, 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 (discrete) modelling offers an interesting framework to
delineate the main dynamical properties of the underlying networks.
Combining graph theoretic concepts and a specific discrete mathematical formalism, we have developed a software suite, GINsim, which facilitates the delineation, the simulation and the analysis of complex regulatory networks [1]. More recently, still on the basis of our generic discrete formal framework, we have implemented a method to assess the dynamical roles of specific regulatory circuits, embedded in complex regulatory networks (demonstrations about the requirement of specific feedback circuits for specific dynamical properties in the discrete framework can be found in [2]). This qualitative modelling approach has already been already applied to various biological systems, in particular to the modelling of genetic modules controlling cell differentiation and pattern formation in the course of early Drosophila development [3]. We are currently applying it to the modelling of the molecular networks controlling the eukaryotic cell cycle [4] and T-lymphocyte differentiation [5]. An overview of recent results will be provided to stimulate a discussion on the assets as well as on the limits of the logical approach. The logical modelling software GINsim, as well as a model library are available in a dedicated XML format (GINML) at the url http://gin.univ-mrs.fr/GINsim. References; 1. Gonzalez AG, Naldi A, Sanchez L, Thieffry D, Chaouiya C (2006). GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. Biosystems 84: 91-100. 2. Remy E, Ruet P, Thieffry D (2006). Positive or negative regulatory circuit inference from multilevel dynamics. Lecture Notes in Control and Information Sciences 341: 263-70. 3. Sa'nchez L, Thieffry D (2003). Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module. Journal of theoretical Biology 224: 517-37. 4. Faure' A, Naldi A, Chaouiya C, Thieffry D (2006). Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics 22: e124-31. 5. Chaouiya R, Remy E, Thieffry D (2006). Qualitative Petri Net modelling of genetic networks. Transactions on Computational Systems Biology 6: 95-112. |