V (2005) Computational techniques for analysis of genetic network dynamics

In this paper we propose modeling and analysis techniques for ge-netic networks that provide biologists with insight into the dynamics of such systems. Central to our modeling approach is the framework of hybrid systems and our analysis tools are derived from formal analysis of such systems. Given a set of states characterizing a prop-erty of biological interestP, we present the Multi-Affine Rectangular Partition (MARP) algorithm for the construction of a set of infeasible states I that will never reach P and the Rapidly Exploring Random Forest of Trees (RRFT) algorithm for the construction of a set of feasible statesF that will reach P. These techniques are scalable to high dimensions and can incorporate uncertainty (partial knowledge of kinetic parameters and state uncertainty). We apply these methods to understand the genetic interactions involved in the phenomenon of luminescence production in the marine bacterium V. fischeri. KEY WORDS—genetic networks, hybrid systems, formal analysis, rapidly-exploring random trees 1