Our model organism is budding yeast (Saccharomyces cerevisiae), one of the best eukaryotes for a systems biology approach to study the evolution of gene networks. We measure and perturb the in vivo dynamics of gene networks using flow cytometry, time-lapse fluorescence microscopy, and yeast molecular genetics. This quantitative biology approach is combined with comparative fungal genomics to glean how novel dynamics and function have evolved in natural gene networks. Fungi are multicellular organisms that have varied ecologies, life cycle strategies, and morphologies. There are many sequenced fungal genomes, and many Fungi are model laboratory organisms with tractable molecular biology and genetics.