From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints
Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic
pathways and have become an established tool for constraint-based modeling and …
pathways and have become an established tool for constraint-based modeling and …
On the feasibility of growth-coupled product synthesis in microbial strains
S Klamt, R Mahadevan - Metabolic engineering, 2015 - Elsevier
Enforcing obligate coupling of growth with synthesis of a desired product has become a key
principle for metabolic engineering of microbial production strains. Various methods from …
principle for metabolic engineering of microbial production strains. Various methods from …
Metabolomics integrated elementary flux mode analysis in large metabolic networks
Elementary flux modes (EFMs) are non-decomposable steady-state pathways in metabolic
networks. They characterize phenotypes, quantify robustness or identify engineering targets …
networks. They characterize phenotypes, quantify robustness or identify engineering targets …
Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth
Traditional (genome-scale) metabolic models of cellular growth involve an approximate
biomass “reaction”, which specifies biomass composition in terms of precursor metabolites …
biomass “reaction”, which specifies biomass composition in terms of precursor metabolites …
Predicting genetic engineering targets with Elementary Flux Mode Analysis: a review of four current methods
Highlights•We briefly review and compare four EFM-based methods for in silico strain
design.•Constrained minimal cut sets and AutoDesign predict deletion targets.•Casop and …
design.•Constrained minimal cut sets and AutoDesign predict deletion targets.•Casop and …
Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections
Abstract Minimal Cut Sets (MCSs) identify sets of reactions which, when removed from a
metabolic network, disable certain cellular functions. The traditional search for MCSs within …
metabolic network, disable certain cellular functions. The traditional search for MCSs within …
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 …
Principal metabolic flux mode analysis
Motivation In the analysis of metabolism, two distinct and complementary approaches are
frequently used: Principal component analysis (PCA) and stoichiometric flux analysis. PCA …
frequently used: Principal component analysis (PCA) and stoichiometric flux analysis. PCA …
TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm
J Pey, JA Villar, L Tobalina, A Rezola, JM García… - …, 2015 - academic.oup.com
Abstract Motivation: Elementary flux modes (EFMs) analysis constitutes a fundamental tool
in systems biology. However, the efficient calculation of EFMs in genome-scale metabolic …
in systems biology. However, the efficient calculation of EFMs in genome-scale metabolic …
Answer Set Programming for Computing Constraints-Based Elementary Flux Modes: Application to Escherichia coli Core Metabolism
Elementary Flux Modes (EFMs) provide a rigorous basis to systematically characterize the
steady state, cellular phenotypes, as well as metabolic network robustness and fragility …
steady state, cellular phenotypes, as well as metabolic network robustness and fragility …