We have used NimbleGen expression arrays to study global gene expression patterns in P. stipitis CBS6054. Unlike S. cerevisiae, which regulates fermentation by sensing the presence of fermentable sugars, P. stipitis induces fermentation in response to oxygen limitation. To examine the effect of carbon source and aeration level on this yeast, we cultivated P. stipitis on glucose or xylose both aerobically and under oxygen limitation in pH controlled bioreactors.  Comparison of gene chip results from these various cultivations will allow for the identification of genes that are induced under oxygen limitation and those that may be affected both by oxygen level and carbon source. We have also examined cellobiose or arabinose as a carbon source, which has revealed highly specific induction patterns in some cases.  These studies will provide invaluable insight into growth on these substrates by P. stipitis and the genes responsible for fermentation of the extremely abundant sugar, xylose. Identification of these genes will yield targets for the future engineering of improved lignocellulose fermenting yeasts.