ArticleBioinformatics (Oxford, England)2014
Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Partial enumeration of extreme rays in metabolic networks using bit pattern trees.Frontiers in bioinformatics · 2026Article
- Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections.NPJ systems biology and applications · 2024Article
- Metabolic modelling links Warburg effect to collagen formation, angiogenesis and inflammation in the tumoral stroma.PloS one · 2024Article
- Unlocking Elementary Conversion Modes: ecmtool Unveils All Capabilities of Metabolic Networks.Patterns (New York, N.Y.) · 2021Article
- Boosting Biomass Quantity and Quality by Improved Mixotrophic Culture of the DiatomFrontiers in plant science · 2021Article
- Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach.Bioinformatics (Oxford, England) · 2020Article
- EFMviz: A COBRA Toolbox extension to visualize Elementary Flux Modes in Genome-Scale Metabolic Models.Metabolites · 2020Article
- Flux tope analysis: studying the coordination of reaction directions in metabolic networks.Bioinformatics (Oxford, England) · 2019Article
- Investigating mixotrophic metabolism in the model diatomPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Article
- Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production.BMC systems biology · 2017Article
- Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms.Nature communications · 2017Article
- From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints.PLoS computational biology · 2017Review
- Algal Cell Factories: Approaches, Applications, and Potentials.Marine drugs · 2016Review
- Which sets of elementary flux modes form thermodynamically feasible flux distributions?The FEBS journal · 2016Article
- In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories.Microbiology and molecular biology reviews : MMBR · 2016Review
- Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome.Biotechnology for biofuels · 2016Article
- Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom.PloS one · 2016Article
- Metabolomics integrated elementary flux mode analysis in large metabolic networks.Scientific reports · 2015Article
- Article
- Computational strategies for a system-level understanding of metabolism.Metabolites · 2014Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
motivationElementary flux mode analysis (EFMA) decomposes complex metabolic network models into tractable biochemical pathways, which have been used for rational design and analysis of metabolic and regulatory networks. However, application of EFMA has often been limited to targeted or simplified metabolic network representations due to computational demands of the method.
resultsDivision of biological networks into subnetworks enables the complete enumeration of elementary flux modes (EFMs) for metabolic models of a broad range of complexities, including genome-scale. Here, subnetworks are defined using serial dichotomous suppression and enforcement of flux through model reactions. Rules for selecting appropriate reactions to generate subnetworks are proposed and tested; three test cases, including both prokaryotic and eukaryotic network models, verify the efficacy of these rules and demonstrate completeness and reproducibility of EFM enumeration. Division of models into subnetworks is demand-based and automated; computationally intractable subnetworks are further divided until the entire solution space is enumerated. To demonstrate the strategy's scalability, the splitting algorithm was implemented using an EFMA software package (EFMTool) and Windows PowerShell on a 50 node Microsoft high performance computing cluster. Enumeration of the EFMs in a genome-scale metabolic model of a diatom, Phaeodactylum tricornutum, identified ∼2 billion EFMs. The output represents an order of magnitude increase in EFMs computed compared with other published algorithms and demonstrates a scalable framework for EFMA of most systems.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.