Switching Gene Regulatory Networks

A fundamental question in biology is how cells change into specific cell types with unique roles throughout development. This process can be viewed as a program prescribing the system dynamics, governed by a network of genetic interactions. Recent experimental evidence suggests that these networks are not fixed but rather change their topology as cells develop. Currently, there are limited tools for the construction and analysis of such self-modifying biological programs. We introduce Switching Gene Regulatory Networks to enable the modeling and analysis of network reconfiguration, and define the synthesis problem of constructing switching networks from observations of cell behavior. We solve the synthesis problem using Satisfiability Modulo Theories (SMT) based methods, and evaluate the feasibility of our method by considering a set of synthetic benchmarks exhibiting typical biological behavior of cell development.