Gene regulatory networks (GRNs) can drive cyclic and temporally ordered processes in biological systems. One of the best-known GRNs of this type is the circadian clock, which drives rhythmic behaviors with a period of approximately 24hrs. The circadian clock network exerts its control, in part, by regulating a dynamic program of gene expression where substantial fractions of the genome are expressed during distinct phases of the circadian cycle. More recently, we have proposed that a different GRN controls the cyclic program of gene expression that is observed during the cell division cycle. In fact, we have observed similar gene expression programs across time scales from hours to days, and across organisms that are evolutionarily diverged by millions of years. These observations suggest that a class of GRNs may serve as central mechanisms that drive temporal gene expression programs in biological systems. One goal of our work is to identify the structure and function of these networks. New approaches for inferring the structure of these GRNs directly from time-series transcriptome data will be discussed. We will also describe experimental and quantitative approaches aimed at probing the dynamics of a GRN that controls the well-ordered, periodic program of transcription observed during the yeast cell-division cycle.