Elementary vectors and conformal sums in polyhedral geometry and their relevance for metabolic pathway analysis
S Müller, G Regensburger - Frontiers in Genetics, 2016 - frontiersin.org
A fundamental result in metabolic pathway analysis states that every flux mode can be
decomposed into a sum of elementary modes. However, only a decomposition without …
decomposed into a sum of elementary modes. However, only a decomposition without …
Towards scaling elementary flux mode computation
While elementary flux mode (EFM) analysis is now recognized as a cornerstone
computational technique for cellular pathway analysis and engineering, EFM application to …
computational technique for cellular pathway analysis and engineering, EFM application to …
Stoichiometric and constraint-based analysis of biochemical reaction networks
Metabolic network analysis based on stoichiometric and constraint-based methods has
become one of the most popular and successful modeling approaches in network and …
become one of the most popular and successful modeling approaches in network and …
Unlocking elementary conversion modes: Ecmtool unveils all capabilities of metabolic networks
The metabolic capabilities of cells determine their biotechnological potential, fitness in
ecosystems, pathogenic threat levels, and function in multicellular organisms. Their …
ecosystems, pathogenic threat levels, and function in multicellular organisms. Their …
Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming
Abstract Motivation Elementary (flux) modes (EMs) have served as a valuable tool for
investigating structural and functional properties of metabolic networks. Identification of the …
investigating structural and functional properties of metabolic networks. Identification of the …
Finding elementary flux modes in metabolic networks based on flux balance analysis and flux coupling analysis: application to the analysis of Escherichia coli …
S Tabe-Bordbar, SA Marashi - Biotechnology letters, 2013 - Springer
Elementary modes (EMs) are steady-state metabolic flux vectors with minimal set of active
reactions. Each EM corresponds to a metabolic pathway. Therefore, studying EMs is helpful …
reactions. Each EM corresponds to a metabolic pathway. Therefore, studying EMs is helpful …
Genome-scale reconstruction of the metabolic network in Pseudomonas stutzeri A1501
Pseudomonas stutzeri A1501 is an endophytic bacterium capable of nitrogen fixation. This
strain has been isolated from the rice rhizosphere and provides the plant with fixed nitrogen …
strain has been isolated from the rice rhizosphere and provides the plant with fixed nitrogen …
Computing elementary flux modes involving a set of target reactions
L David, A Bockmayr - IEEE/ACM transactions on …, 2014 - ieeexplore.ieee.org
Elementary flux mode (EM) computation is an important tool in the constraint-based analysis
of genome-scale metabolic networks. Due to the combinatorial complexity of these networks …
of genome-scale metabolic networks. Due to the combinatorial complexity of these networks …
Computing irreversible minimal cut sets in genome-scale metabolic networks via flux cone projection
A Röhl, T Riou, A Bockmayr - Bioinformatics, 2019 - academic.oup.com
Abstract Motivation Minimal cut sets (MCSs) for metabolic networks are sets of reactions
which, if they are removed from the network, prevent a target reaction from carrying flux. To …
which, if they are removed from the network, prevent a target reaction from carrying flux. To …
EFMlrs: a Python package for elementary flux mode enumeration via lexicographic reverse search
BA Buchner, J Zanghellini - BMC bioinformatics, 2021 - Springer
Background Elementary flux mode (EFM) analysis is a well-established, yet computationally
challenging approach to characterize metabolic networks. Standard algorithms require huge …
challenging approach to characterize metabolic networks. Standard algorithms require huge …