2012/08/09 by Christian Jungreuthmayer, Jungreuthmayer, Christian, David E. Ruckerbauer +3
Biochemistry, Genetics and Molecular Biology · Engineering · #92C42 #Biofuel production and bioconversion #FOS: Biological sciences #Gene Regulatory Network Analysis #Microbial Metabolic Engineering and Bioproduction #Molecular Networks (q-bio.MN) #msc:92C42 #q-bio.MN
paper · pdf · doi:10.48550/arxiv.1208.1853
7 pages, 2 figures, 13 tables; prepared for submission to Bioinformatics
arxiv created 2012/08/09 · openalex publication_date 2012/08/09 · arxiv updated 2012/08/10 · openalex created_date 2022/08/30 · openalex updated_date 2026/07/28
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.