Recent findings of a genome-wide oscillation involving the transcriptome of the budding yeast Saccharomyces cerevisiae suggest that the most promising path to an understanding of the cell as a dynamic system will proceed from carefully designed time-series sampling followed by the development of signal-processing methods suited to molecular biological datasets. When everything oscillates, conventional biostatistical approaches fall short in identifying functional relationships among genes and their transcripts. Worse, based as they are on steady-state assumptions, such approaches may be misleading. In this chapter, we describe the continuous gated synchrony system and the experiments leading to the concept of genome-wide oscillations, and suggest methods of analysis better suited to dissection of oscillating systems. Using a yeast continuous-culture system, the most precise and stable biological system extant, we explore analytical tools such as wavelet multiresolution decomposition, Fourier analysis, and singular value decomposition to uncover the dynamic architecture of phenotype.