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Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks

  • Aurélien Naldi
  • Denis Thieffry
  • Claudine Chaouiya
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4695)

Abstract

The complexity of biological regulatory networks calls for the development of proper mathematical methods to model their structures and to obtain insight in their dynamical behaviours. One qualitative approach consists in modelling regulatory networks in terms of logical equations (using either Boolean or multi-valued discretisation).

In this paper, we propose a novel implementation of the generalised logical formalism by means of Multi-valued Decision Diagrams. We show that the use of this representation enables the development of efficient algorithms for the analysis of specific dynamical properties of the regulatory graphs. In particular, we address the question of determining conditions insuring the functionality of feedback circuits, as well as the identification of stable states. Finally, we apply these algorithms to logical models of T cell activation and differentiation.

Keywords

Regulatory networks logical modelling decision diagrams regulatory circuits stable states 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Aurélien Naldi
    • 1
  • Denis Thieffry
    • 1
  • Claudine Chaouiya
    • 1
  1. 1.TAGC, INSERM ERM206, Université de la Méditerranée, MarseillesFrance

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