ReviewFEMS microbiology reviews2009
Genome-scale models of bacterial metabolism: reconstruction and applications.
Review in FEMS microbiology reviews, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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Who cites it
117 citing papers in PubMed.
- Thermodynamic metabolic modeling of growth and bioproduction potential of the acetogenSynthetic and systems biotechnology · 2026Article
- Selecting methods for draft GEM generation in multicellular eukaryotes: a comparative analysis.BMC bioinformatics · 2026Article
- Sec and Tat Mediated Secretion Safeguards Mycobacterium tuberculosis Membrane Homeostasis.Molecular & cellular proteomics : MCP · 2026Article
- Evaluation of Genome-Scale Model Reconstruction Strategies forMetabolites · 2025Article
- microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis.Genome biology · 2025Article
- Competition and cooperation: The plasticity of bacterial interactions across environments.PLoS computational biology · 2025Article
- Article
- Enhancing genome-scale metabolic models with kinetic data: resolving growth and citramalate production trade-offs inBioinformatics advances · 2025Article
- Unraveling the metabolic landscape of Exophiala spinifera strain FM: Model reconstruction, insights into biodesulfurization and beyond.PloS one · 2025Article
- Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective.Metabolites · 2024Review
- Using metabolic networks to predict cross-feeding and competition interactions between microorganisms.Microbiology spectrum · 2024Article
- Metabolic compatibility and the rarity of prokaryote endosymbioses.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Model-based dynamic engineering ofBiotechnology notes (Amsterdam, Netherlands) · 2022Article
- Evolutionary Divergence ofFrontiers in microbiology · 2022Article
- Cell Growth Model with Stochastic Gene Expression Helps Understand the Growth Advantage of Metabolic Exchange and Auxotrophy.mSystems · 2021Article
- Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions.Microbial cell factories · 2021Article
- The metabolic network of the last bacterial common ancestor.Communications biology · 2021Article
- Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Omics-Driven Biotechnology for Industrial Applications.Frontiers in bioengineering and biotechnology · 2021Review
- Metagenomics for taxonomy profiling: tools and approaches.Bioengineered · 2020Article
57 more citing papers are in PubMed but not listed here.
Corrections and comments
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-scale metabolic models bridge the gap between genome-derived biochemical information and metabolic phenotypes in a principled manner, providing a solid interpretative framework for experimental data related to metabolic states, and enabling simple in silico experiments with whole-cell metabolism. Models have been reconstructed for almost 20 bacterial species, so far mainly through expert curation efforts integrating information from the literature with genome annotation. A wide variety of computational methods exploiting metabolic models have been developed and applied to bacteria, yielding valuable insights into bacterial metabolism and evolution, and providing a sound basis for computer-assisted design in metabolic engineering. Recent advances in computational systems biology and high-throughput experimental technologies pave the way for the systematic reconstruction of metabolic models from genomes of new species, and a corresponding expansion of the scope of their applications. In this review, we provide an introduction to the key ideas of metabolic modeling, survey the methods, and resources that enable model reconstruction and refinement, and chart applications to the investigation of global properties of metabolic systems, the interpretation of experimental results, and the re-engineering of their biochemical capabilities.
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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.