ReviewMolecular systems biology2009
Applications of genome-scale metabolic reconstructions.
Review in Molecular systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 391 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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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
391 citing papers in PubMed.
- Thermodynamic metabolic modeling of growth and bioproduction potential of the acetogenSynthetic and systems biotechnology · 2026Article
- An adenylyl cyclase switch reroutes carbon from growth to virulence lipids inbioRxiv : the preprint server for biology · 2026Article
- AlphaGEM enables precise genome-scale metabolic modelling by integrating protein structure alignment with deep-learning-based dark metabolism mining.Nature communications · 2026Article
- A systems-level view of metabolic impact of copper and methane valorization potential inMetabolic engineering communications · 2026Article
- Hypergraph learning with multi-dimensional metabolite feature extractions and static-dynamic attention mechanisms to fill missing reactions in metabolic networks.Briefings in bioinformatics · 2026Article
- Defining metabolic niches for marine microbial heterotrophs.Science advances · 2026Article
- A Novel Topology-Based Candidate Reaction Prediction Approach for Gap-Fillings of Genome-Scale Metabolic Models.Metabolites · 2026Article
- Systematic data-driven genome-scale metabolic model reduction for bioprocess modeling: CHO culture case study.NPJ systems biology and applications · 2026Article
- Article
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- GEMCAT-a new algorithm for gene expression-based prediction of metabolic alterations.NAR genomics and bioinformatics · 2025Article
- Genome-scale models in human metabologenomics.Nature reviews. Genetics · 2025Review
- Metadag: a web tool to generate and analyse metabolic networks.BMC bioinformatics · 2025Article
- Unraveling the metabolic landscape of Exophiala spinifera strain FM: Model reconstruction, insights into biodesulfurization and beyond.PloS one · 2025Article
- Strategy for Optimizing Vitamin B12 Production inMetabolites · 2024Article
- Metabolic modelling as a powerful tool to identify critical components of Pneumocystis growth medium.PLoS computational biology · 2024Article
- Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling.PLoS pathogens · 2024Article
- Machine learning: an advancement in biochemical engineering.Biotechnology letters · 2024Review
- Community metabolic modeling of host-microbiota interactions through multi-objective optimization.iScience · 2024Article
- Genome-scale model ofMicrobiology spectrum · 2024Article
331 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
The availability and utility of genome-scale metabolic reconstructions have exploded since the first genome-scale reconstruction was published a decade ago. Reconstructions have now been built for a wide variety of organisms, and have been used toward five major ends: (1) contextualization of high-throughput data, (2) guidance of metabolic engineering, (3) directing hypothesis-driven discovery, (4) interrogation of multi-species relationships, and (5) network property discovery. In this review, we examine the many uses and future directions of genome-scale metabolic reconstructions, and we highlight trends and opportunities in the field that will make the greatest impact on many fields of biology.
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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.