ReviewNature reviews. Microbiology2012
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.
Review in Nature reviews. Microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 380 papers.
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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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Who cites it
380 citing papers in PubMed.
- EINN: An enzyme-informed neural network guided by an enzyme-constrained genome-scale metabolic model.Synthetic and systems biotechnology · 2027Article
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- EHMN 2026: A Thermodynamically Refined, SBML-Standardised Human Metabolic Network for Genome-Scale Analysis and QSP Integration.Metabolites · 2026Article
- Enhancing Synthesis Efficiency in Microbial 1,5-Pentanediol Production Through Transcriptomics-Informed Metabolic Engineering ofMicroorganisms · 2026Article
- Model-driven exploration of lactose and galactose metabolism via an oxidoreductive pathway in Sungouiella intermedia for cell factory applications.Microbial cell factories · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Reduced glutathione levels inmSystems · 2026Article
- A guide to network analysis, multi-omics integration, and applications in livestock microbiome research.World journal of microbiology & biotechnology · 2025Review
- Global constraint principle for microbial growth laws.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A Review of the Progress in the Microbial Biosynthesis of Prenylated Aromatic Compounds.Molecules (Basel, Switzerland) · 2025Review
- Metabolism-dependent succinylation governs resource allocation for antibiotic resistance.Science advances · 2025Article
- Metabolic reprogramming and functional crosstalk within the tumor microenvironment (TME) and A Multi-omics anticancer approach.Medical oncology (Northwood, London, England) · 2025Review
- Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.Briefings in bioinformatics · 2025Review
- The Evolution of Systems Biology and Systems Medicine: From Mechanistic Models to Uncertainty Quantification.Annual review of biomedical engineering · 2025Review
- The Strategy and Application of Gene Attenuation in Metabolic Engineering.Microorganisms · 2025Review
- MACAW: a method for semi-automatic detection of errors in genome-scale metabolic models.Genome biology · 2025Article
- Comprehensive evaluation of the capacities of microbial cell factories.Nature communications · 2025Article
320 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Reconstructed microbial metabolic networks facilitate a mechanistic description of the genotype-phenotype relationship through the deployment of constraint-based reconstruction and analysis (COBRA) methods. As reconstructed networks leverage genomic data for insight and phenotype prediction, the development of COBRA methods has accelerated following the advent of whole-genome sequencing. Here, we describe a phylogeny of COBRA methods that has rapidly evolved from the few early methods, such as flux balance analysis and elementary flux mode analysis, into a repertoire of more than 100 methods. These methods have enabled genome-scale analysis of microbial metabolism for numerous basic and applied uses, including antibiotic discovery, metabolic engineering and modelling of microbial community behaviour.
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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.