ArticlePatterns (New York, N.Y.)2021
Unlocking Elementary Conversion Modes: ecmtool Unveils All Capabilities of Metabolic Networks.
Article in Patterns (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- In silico analysis and comparison of the metabolic capabilities of different organisms by reducing metabolic complexity.Microbiome · 2026Article
- Stoichiometric analysis of microbial communities links function, structure, and biomass carrying capacity.The ISME journal · 2026Review
- A compact model of Escherichia coli core and biosynthetic metabolism.PLoS computational biology · 2025Article
- A hierarchy of metabolite exchanges in metabolic models of microbial species and communities.PLoS computational biology · 2024Article
- Microbial Pathway Thermodynamics: Stoichiometric Models Unveil Anabolic and Catabolic Processes.Life (Basel, Switzerland) · 2024Article
- ecmtool: fast and memory-efficient enumeration of elementary conversion modes.Bioinformatics (Oxford, England) · 2023Article
- EFMlrs: a Python package for elementary flux mode enumeration via lexicographic reverse search.BMC bioinformatics · 2021Article
- Metabolic control of nitrogen fixation in rhizobium-legume symbioses.Science advances · 2021Article
- Understanding FBA Solutions under Multiple Nutrient Limitations.Metabolites · 2021Article
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Authors and funding
6 authors.
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Abstract
The metabolic capabilities of cells determine their biotechnological potential, fitness in ecosystems, pathogenic threat levels, and function in multicellular organisms. Their comprehensive experimental characterization is generally not feasible, particularly for unculturable organisms. In principle, the full range of metabolic capabilities can be computed from an organism's annotated genome using metabolic network reconstruction. However, current computational methods cannot deal with genome-scale metabolic networks. Part of the problem is that these methods aim to enumerate all metabolic pathways, while computation of all (elementally balanced) conversions between nutrients and products would suffice. Indeed, the elementary conversion modes (ECMs, defined by Urbanczik and Wagner) capture the full metabolic capabilities of a network, but the use of ECMs has not been accessible until now. We explain and extend the theory of ECMs, implement their enumeration in ecmtool, and illustrate their applicability. This work contributes to the elucidation of the full metabolic footprint of any cell.
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