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 …
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 …
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 …
Computing optimal factories in metabolic networks with negative regulation
S Krieger, J Kececioglu - Bioinformatics, 2022 - academic.oup.com
Motivation A factory in a metabolic network specifies how to produce target molecules from
source compounds through biochemical reactions, properly accounting for reaction …
source compounds through biochemical reactions, properly accounting for reaction …
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 …
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 …
Flux tope analysis: studying the coordination of reaction directions in metabolic networks
Motivation Elementary flux mode (EFM) analysis allows an unbiased description of
metabolic networks in terms of minimal pathways (involving a minimal set of reactions). To …
metabolic networks in terms of minimal pathways (involving a minimal set of reactions). To …
Which sets of elementary flux modes form thermodynamically feasible flux distributions?
Elementary flux modes (EFMs) are non‐decomposable steady‐state fluxes through
metabolic networks. Every possible flux through a network can be described as a …
metabolic networks. Every possible flux through a network can be described as a …
Robust Optimal Metabolic Factories
S Krieger, J Kececioglu - Journal of Computational Biology, 2024 - liebertpub.com
Perhaps the most fundamental model in synthetic and systems biology for inferring
pathways in metabolic reaction networks is a metabolic factory: a system of reactions that …
pathways in metabolic reaction networks is a metabolic factory: a system of reactions that …
Algorithmic Inference of Cellular Reaction Pathways and Protein Secondary Structure
S Krieger - 2022 - search.proquest.com
Proteins are biological molecules that carry out a multitude of cellular functions. Their
function is largely determined by the shape of the folded molecule within the cell—called …
function is largely determined by the shape of the folded molecule within the cell—called …