ArticleNature protocols2010
A protocol for generating a high-quality genome-scale metabolic reconstruction.
Article in Nature protocols, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 870 papers, 1 of them a synthesis that pooled it.
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Who cites it
870 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Leveraging genome-scale metabolic models to understand aerobic methanotrophs.The ISME journal · 2024Pooled it
- EINN: An enzyme-informed neural network guided by an enzyme-constrained genome-scale metabolic model.Synthetic and systems biotechnology · 2027Article
- BioEMMA: Automated Generation of Model-Specific Escher-Compatible Maps from KEGG Pathways.Biology · 2026Article
- Systems Biology and Structure-Based In Silico Evaluations of Quercetin-Psychobiotic Interactions for the Management of Depression.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Environmental formermSystems · 2026Article
- Annotating the pangenome reveals the diversity in the genetic basis for metabolic enzymes.Science advances · 2026Article
- An anaerobic pathogen rewires host metabolism to fuel oxidative growth in the inflamed gut.Cell · 2026Article
- A community reconstruction of Chinese hamster metabolism and structural systems biology elucidate metabolic rewiring in lactate-free CHO cells.Cell systems · 2026Article
- Integrated multi-dimensional modeling of non-model bacteria identifies engineering targets for acarbose biosynthesis optimization.Cell reports methods · 2026Article
- Nutrient control enables metabolic reconstruction ofbioRxiv : the preprint server for biology · 2026Article
- XomicsToModel: omics data integration and generation of thermodynamically consistent metabolic models.Nature protocols · 2026Article
- Selecting methods for draft GEM generation in multicellular eukaryotes: a comparative analysis.BMC bioinformatics · 2026Article
- Enzyme-constrained genome-scale modeling resolves growth-production trade-offs in fermentative biohydrogen production.Environmental science and ecotechnology · 2026Article
- Keystone concept revisited: insights into microbial community dynamics and control.Nature reviews. Microbiology · 2026Review
- Incorporation of Cryptic Plasmid Energetics Improves Genome-Scale Metabolic Predictions in Probiotic E. coli Nissle 1917.Microbial biotechnology · 2026Article
- High-throughput generation and comparison of genome-scale metabolic models reveal strain-specific metabolic diversity in 439mSystems · 2026Article
- Multi-strain analysis ofmSystems · 2026Article
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- Understanding plant resilience by putting photosynthesis and photorespiration in the metabolic context.Planta · 2026Review
- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
810 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have been developed over the last 10 years. These reconstructions represent structured knowledge bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates a myriad of computational biological studies, including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge bases. Here we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction, as well as the common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process.
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Registered trials
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.