ArticleScientific reports2018
Enumerating all possible biosynthetic pathways in metabolic networks.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Evaluating Metabolic Support in Pairwise Microbial Communities Using MetQuest.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Article
- Before LUCA: unearthing the chemical roots of metabolism.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- AEPMA: peptide-microbe association prediction based on autoevolutionary heterogeneous graph learning.Briefings in bioinformatics · 2025Article
- Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes.Nature communications · 2024Article
- Endophytic fungi: A future prospect for breast cancer therapeutics and drug development.Heliyon · 2024Review
- Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass.Journal of industrial microbiology & biotechnology · 2024Review
- Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes.ISME communications · 2023Article
- Metabolic modeling of the International Space Station microbiome reveals key microbial interactions.Microbiome · 2022Article
- Endophytic Fungi: Key Insights, Emerging Prospects, and Challenges in Natural Product Drug Discovery.Microorganisms · 2022Review
- Finding branched pathways in metabolic network via atom group tracking.PLoS computational biology · 2021Article
- Modelling microbial communities: Harnessing consortia for biotechnological applications.Computational and structural biotechnology journal · 2021Review
- Integrative Modeling of Gene Expression and Metabolic Networks ofFrontiers in plant science · 2021Article
- Deep learning approaches for natural product discovery from plant endophytic microbiomes.Environmental microbiome · 2021Review
- Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks.Nucleic acids research · 2020Article
- The Large Scale Structure of Human Metabolism Reveals Resilience via Extensive Signaling Crosstalk.Frontiers in physiology · 2020Article
- Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments.Computational and structural biotechnology journal · 2020Article
- Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review.Frontiers in microbiology · 2019Review
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3 authors.
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Abstract
Exhaustive identification of all possible alternate pathways that exist in metabolic networks can provide valuable insights into cellular metabolism. With the growing number of metabolic reconstructions, there is a need for an efficient method to enumerate pathways, which can also scale well to large metabolic networks, such as those corresponding to microbial communities. We developed MetQuest, an efficient graph-theoretic algorithm to enumerate all possible pathways of a particular size between a given set of source and target molecules. Our algorithm employs a guided breadth-first search to identify all feasible reactions based on the availability of the precursor molecules, followed by a novel dynamic-programming based enumeration, which assembles these reactions into pathways of a specified size producing the target from the source. We demonstrate several interesting applications of our algorithm, ranging from identifying amino acid biosynthesis pathways to identifying the most diverse pathways involved in degradation of complex molecules. We also illustrate the scalability of our algorithm, by studying large graphs such as those corresponding to microbial communities, and identify several metabolic interactions happening therein. MetQuest is available as a Python package, and the source codes can be found at https://github.com/RamanLab/metquest .
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