ArticleNature protocols2020
A workflow for generating multi-strain genome-scale metabolic models of prokaryotes.
Article in Nature protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- XomicsToModel: omics data integration and generation of thermodynamically consistent metabolic models.Nature protocols · 2026Article
- High-throughput generation and comparison of genome-scale metabolic models reveal strain-specific metabolic diversity in 439mSystems · 2026Article
- Multi-strain analysis ofmSystems · 2026Article
- MCC: automated mass and charge curation at the genome scale applied toMicrobiology spectrum · 2026Article
- Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models.mSystems · 2026Article
- Exploring the IS-capades ofMicrobial genomics · 2026Article
- Predicting Strain-Specific Metabolic Capabilities in the GenusComputational and structural biotechnology journal · 2026Article
- Multi-strain Analysis ofbioRxiv : the preprint server for biology · 2025Article
- Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.Briefings in bioinformatics · 2025Review
- Influence of Amino Acids on Quorum Sensing-Related Pathways inMetabolites · 2025Article
- Pan-genome-scale metabolic modeling ofmSystems · 2024Article
- Interspecies synergistic interactions mediated by cofactor exchange enhance stress tolerance by inducing biofilm formation.mSystems · 2024Article
- Refining microbial community metabolic models derived from metagenomics using reference-based taxonomic profiling.mSystems · 2024Article
- A dual-scale fused hypergraph convolution-based hyperedge prediction model for predicting missing reactions in genome-scale metabolic networks.Briefings in bioinformatics · 2024Article
- Pangenome reconstruction ofmSystems · 2024Article
- Using metabolic networks to predict cross-feeding and competition interactions between microorganisms.Microbiology spectrum · 2024Article
- Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0.Nature protocols · 2024Review
- A validated pangenome-scale metabolic model for theMicrobial genomics · 2024Article
- Genome-scale metabolic models applied for human health and biopharmaceutical engineering.Quantitative biology (Beijing, China) · 2023Review
- Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models.eLife · 2023Article
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Authors and funding
5 authors.
Funding
Abstract
Genome-scale models (GEMs) of bacterial strains' metabolism have been formulated and used over the past 20 years. Recently, with the number of genome sequences exponentially increasing, multi-strain GEMs have proved valuable to define the properties of a species. Here, through four major stages, we extend the original Protocol used to generate a GEM for a single strain to enable multi-strain GEMs: (i) obtain or generate a high-quality model of a reference strain; (ii) compare the genome sequence between a reference strain and target strains to generate a homology matrix; (iii) generate draft strain-specific models from the homology matrix; and (iv) manually curate draft models. These multi-strain GEMs can be used to study pan-metabolic capabilities and strain-specific differences across a species, thus providing insights into its range of lifestyles. Unlike the original Protocol, this procedure is scalable and can be partly automated with the Supplementary Jupyter notebook Tutorial. This Protocol Extension joins the ranks of other comparable methods for generating models such as CarveMe and KBase. This extension of the original Protocol takes on the order of weeks to multiple months to complete depending on the availability of a suitable reference model.
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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.