Animal development starts from a single cell called the fertilized egg. The fertilized egg contains all the instructions needed to build a complicated organism, giving rise to a wide variety of distinct cell types with specialized functions. What has orchestrated this marvelous construction of such a complex life form? To begin to address this question, we need to understand how the different cell types are specified. Transcriptional regulation of gene expression has been shown to be a crucial mechanism in the specification process. Mathematical models of the transcriptional regulatory networks enable us to examine animal development from a dynamical system perspective, and allow us to make quantitative predictions, thereby enhancing our understanding of the organization and design principles of the regulatory system. Here I discuss selected mathematical models built for the fruit fly Drosophila melanogaster and the Sea urchin Strongylocentrotus purpuratus/Lytechinus variegatus embryonic development, a hypothesis derived from modeling studies and its potential applications in regenerative medicine.