  Despite the significant progress made in recent years, the computation of the
complete set of elementary flux modes of large or even genome-scale metabolic
networks is still impossible. We introduce a novel approach to speed up the
calculation of elementary flux modes by including transcriptional regulatory
information into the analysis of metabolic network. Taking into account gene
regulation dramatically reduces the solution space and allows the presented
algorithm to constantly eliminate biologically infeasible modes at an early
stage of the computation procedure. Thereby, the computational costs, such as
runtime, memory usage and disk space are considerably reduced. Consequently,
using the presented mode elimination algorithm pushes the size of metabolic
networks that can be studied by elementary flux modes to new limits.
