ReviewMolecular systems biology2013
Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.
Review in Molecular systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 141 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
141 citing papers in PubMed, 1 synthesis or guideline pooled it.
- On the Origin of Biomolecular Networks.Frontiers in genetics · 2019Pooled it
- Advances in genome-scale metabolic modeling of Bacillus subtilis.Biotechnology letters · 2026Review
- AI-enabled fungal biomanufacturing: from genome mining to the artificial intelligence virtual cell.Mycology · 2026Review
- Mechanistic insights into sodium citrate-induced metabolic rewiring for enhanced S-adenosylmethionine synthesis via transcriptomics and constraint-based modeling.Bioprocess and biosystems engineering · 2026Article
- Effect of Thioredoxin Tag, Oxidizing Environment, and Temperature on the Global Metabolome of E. Coli Strains.Applied biochemistry and biotechnology · 2026Article
- The EcoCyc database (2025).EcoSal Plus · 2025Review
- Article
- Exploring interspecific interaction variability in microbiota: A review.Engineering microbiology · 2024Review
- Understanding flux switching in metabolic networks through an analysis of synthetic lethals.NPJ systems biology and applications · 2024Article
- Article
- Using metabolic networks to predict cross-feeding and competition interactions between microorganisms.Microbiology spectrum · 2024Article
- Recent advances in genome-scale engineering inEngineering microbiology · 2024Review
- Article
- The EcoCyc Database (2023).EcoSal Plus · 2023Review
- From Spatial-Temporal Multiscale Modeling to Application: Bridging the Valley of Death in Industrial Biotechnology.Bioengineering (Basel, Switzerland) · 2023Review
- Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes.ISME communications · 2023Article
- Model-driven experimental design workflow expands understanding of regulatory role of Nac inNAR genomics and bioinformatics · 2023Article
- Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.Plants (Basel, Switzerland) · 2022Review
- Metabolic modeling of the International Space Station microbiome reveals key microbial interactions.Microbiome · 2022Article
- The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility.PLoS computational biology · 2022Article
81 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The genome-scale model (GEM) of metabolism in the bacterium Escherichia coli K-12 has been in development for over a decade and is now in wide use. GEM-enabled studies of E. coli have been primarily focused on six applications: (1) metabolic engineering, (2) model-driven discovery, (3) prediction of cellular phenotypes, (4) analysis of biological network properties, (5) studies of evolutionary processes, and (6) models of interspecies interactions. In this review, we provide an overview of these applications along with a critical assessment of their successes and limitations, and a perspective on likely future developments in the field. Taken together, the studies performed over the past decade have established a genome-scale mechanistic understanding of genotype-phenotype relationships in E. coli metabolism that forms the basis for similar efforts for other microbial species. Future challenges include the expansion of GEMs by integrating additional cellular processes beyond metabolism, the identification of key constraints based on emerging data types, and the development of computational methods able to handle such large-scale network models with sufficient accuracy.
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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.