Recent advances in gene sequencing technology are now shedding light on the complex interplay between genes that elicit phenotypic behavior characteristic of any given organism. In order to mediate internal and external signals, the daunting task of classifying an organism’s genes into complex signaling pathways needs to be completed. The Handbook of Research on Computational Methodologies in Gene Regulatory Networks focuses on methods widely used in modeling gene networks including structure discovery, learning, and optimization. This innovative Handbook of Research presents a complete overview of computational intelligence approaches for learning and optimization and how they can be used in gene regulatory networks.