Modeling the Molecular Network Controlling Adhesion Between Human Endothelial Cells: Inference and Simulation Using Constraint Logic Programming

Abstract

Abstract. Cell-cell adhesion plays a critical role in the formation of tissues and organs. Adhesion between endothelial cells is also involved in the control of leukocyte migration across the endothelium of blood vessels. The most important players in this process are probably identified and the overall organization of the biochemical network can be drawn, but knowledge about connectivity is still incomplete, and the numerical values of kinetic parameters are unknown. This calls for qualitative modeling methods. Our aim in this paper is twofold: (i) to integrate in a unified model the biochemical network and the genetic circuitry. For this purpose we transform our system into a system of piecewise linear differential equations and then use Thomas theory of discrete networks.(ii) to show how constraints can be used to infer ranges of parameter values from observations and, with the same model, perform qualitative simulations.

Modeling Biological Networks by Action Languages via Answer Set Programming

“…Constraint programming as such has already been applied to many biological problems, as best witnessed by the proceedings of the workshop series on Constraint Based Methods for Bioinformatics as well as this special issue of the Constraint Journal at hand. Among many others, we find Fanchon et al [14], Backofen et al [1], and Eveillard et al [13].…”

Reverse engineering and verification of gene networks: Principles, assumptions, and limitations of present methods and future perspectives

“…In this context, methods that infer qualitatively the dynamics of the network without detailed kinetic parameters might be of interest. For example, the so-called constraints logic programming represents a realistic way (step in between) toward an understanding of the dynamics of networks (Corblin et al, 2007;Fanchon et al, 2004).…”

Connections and Integration with SAT Solvers: A Survey and a Case Study in Computational Biology

“…This formalism has been proposed from the beginning of GRN studies [105]. It has largely been applied to the analysis of GRNs, for example, those described in [35,47,96,104] or those described in [57,58,92], which use a very similar discrete formalism.…”