The Microbial Synthetic Biology lab at the Great Lakes Bioenergy Research Center is a multi-disciplinary research unit tasked with surmounting the bottlenecks in cellulosic biofuel production. One developmental pipeline used in our laboratory consists of a high-throughput screening platform coupled with rapid bioreactor characterization of promising organisms. Using this paradigm, libraries of candidate strains (either from strain collections or from rationally-developed genetic libraries) are rapidly screened for favorable phenotypes and winnowed to a smaller number of promising isolates. These isolates are then examined in controlled bioreactors with working volumes ranging from 5mL to 10L. Data from these bioreactors are gathered in order do assess fermentation performance as well as to perform “multi-omic” analysis of the strains. Here, we describe our use of this research pipeline for screening a collection of wild and industrial Saccharomyces cerevisiae yeast strains and for subsequent characterization of candidate strains.