Bacteria have evolved the ability to efficiently and resourcefully adapt to changing environments. A key means by which they optimize their use of available nutrients is through adjustments in gene expression with consequent changes in enzyme activity. We report a new method for drawing environmental inferences from gene expression data. Our method prioritizes a list of candidate carbon sources for their compatibility with a gene expression profile using the framework of flux balance analysis to model the organism's metabolic network.
Brandes, A., Lun, D. S., Ip, K., Zucker, J., Colijn, C., Weiner, B., & Galagan, J. E. (2012). Inferring carbon sources from gene expression profiles using metabolic flux models. PLoS ONE, 7(5). https://doi.org/10.1371/journal.pone.0036947