The use of predictive modeling in the analysis of gene expression data can greatly accelerate the pace of scientific discovery in biomedical research by enabling in silico experimentation to test disease triggers and potential drug therapies. Techniques such as agent-based modeling and multi-agent simulations are of particular interest as they support the discovery of emergent pathways, as opposed to other dynamic modeling approaches such as dynamic Bayesian nets and system dynamics. Thus far, emergence-modeling techniques have been primarily applied at the multi-cellular level, or have focused on signaling and metabolic networks. We present an approach where emergence modeling is extended to regulatory networks and demonstrate its application to the discovery of neuroprotective pathways. An initial evaluation of the approach indicates that emergence modeling provides novel insights for the analysis of regulatory networks which can advance the discovery of acute treatments for stroke and other diseases.