In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories
Shifting from chemical to biotechnological processes is one of the cornerstones of 21st
century industry. The production of a great range of chemicals via biotechnological means is …
century industry. The production of a great range of chemicals via biotechnological means is …
Elementary flux modes in a nutshell: properties, calculation and applications
Elementary flux mode (EFM) analysis allows the unbiased decomposition of a metabolic
network into minimal functional units, making it a powerful tool for metabolic engineering …
network into minimal functional units, making it a powerful tool for metabolic engineering …
Elucidating plant-microbe-environment interactions through omics-enabled metabolic modelling using synthetic communities
With a growing world population and increasing frequency of climate disturbance events, we
are in dire need of methods to improve plant productivity, resilience, and resistance to both …
are in dire need of methods to improve plant productivity, resilience, and resistance to both …
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 …
Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition
Motivation: Elementary flux mode analysis (EFMA) decomposes complex metabolic network
models into tractable biochemical pathways, which have been used for rational design and …
models into tractable biochemical pathways, which have been used for rational design and …
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 …
tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks
Elementary flux modes (EFMs) are important structural tools for the analysis of metabolic
networks. It is known that many topologically feasible EFMs are biologically irrelevant …
networks. It is known that many topologically feasible EFMs are biologically irrelevant …
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 …
Green pathways: metabolic network analysis of plant systems
LM Dersch, V Beckers, C Wittmann - Metabolic engineering, 2016 - Elsevier
Metabolic engineering of plants with enhanced crop yield and value-added compositional
traits is particularly challenging as they probably exhibit the highest metabolic network …
traits is particularly challenging as they probably exhibit the highest metabolic network …
Minimizing enzyme mass to decompose flux distribution for identifying biologically relevant elementary flux modes
J Chen, Y Huang, C Zhong - Biosystems, 2023 - Elsevier
The flux distribution in metabolic network can be decomposed as non-negative linear
combinations of elementary flux modes (EFMs). Identifying biologically relevant EFM …
combinations of elementary flux modes (EFMs). Identifying biologically relevant EFM …