Achievement

IGERT trainee Sara Collins is author in:

S. Collins, E. Reznik, and D. Segrè, Temporal expression-based analysis of metabolism, PLoS Comput. Biol. 8(11): e1002781.

Metabolic flux is frequently rerouted through cellular metabolism in response to dynamic changes in the intra- and extra-cellular environment. To capture the mechanisms underlying these metabolic transitions we perform a Temporal Expression-based Analysis of Metabolism (TEAM). We apply TEAM to understanding the dynamics of Shewanella oneidensis grown under aerobic, lactate-limited conditions using time-series gene expression data and a large reference compendium of gene expression. We study the sensitivity of TEAM to changes in its fundamental free parameter θ, and reveal that discrete zones of distinct metabolic behavior arise as this parameter is changed and we are able to constrain the range of θ to a small, well-defined interval. We observe that small errors early in the simulation propagate to relatively large changes later.