ReviewNature biotechnology2008
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.
Review in Nature biotechnology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 232 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
232 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Leveraging genome-scale metabolic models to understand aerobic methanotrophs.The ISME journal · 2024Pooled it
- Metabolic remodeling of microorganisms by mobile genetic elements alters mutualistic community composition.mSystems · 2025Article
- Genome-scale metabolic modeling reveals specific vaginalMicrobiology spectrum · 2025Article
- New insights in metabolism modelling to decipher plant-microbe interactions.The New phytologist · 2025Review
- Moving from genome-scale to community-scale metabolic models for the human gut microbiome.Nature microbiology · 2025Review
- Hierarchical metabolic engineering for rewiring cellular metabolism.FEMS microbiology reviews · 2025Review
- Article
- Metabolic modelling as a powerful tool to identify critical components of Pneumocystis growth medium.PLoS computational biology · 2024Article
- Using metabolic networks to predict cross-feeding and competition interactions between microorganisms.Microbiology spectrum · 2024Article
- Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony.PLoS computational biology · 2023Article
- Model-driven experimental design workflow expands understanding of regulatory role of Nac inNAR genomics and bioinformatics · 2023Article
- Biosensor-assisted titratable CRISPRi high-throughput (BATCH) screening for over-production phenotypes.Metabolic engineering · 2023Article
- Multi-scale model suggests the trade-off between protein and ATP demand as a driver of metabolic changes during yeast replicative ageing.PLoS computational biology · 2022Article
- The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility.PLoS computational biology · 2022Article
- Bottom-up synthetic ecology study of microbial consortia to enhance lignocellulose bioconversion.Biotechnology for biofuels and bioproducts · 2022Review
- The choice of the objective function in flux balance analysis is crucial for predicting replicative lifespans in yeast.PloS one · 2022Article
- CerealESTDb: A Comprehensive Resource for Abiotic Stress-Responsive Annotated ESTs With Predicted Genes, Gene Ontology, and Metabolic Pathways in Major Cereal Crops.Frontiers in genetics · 2022Article
- Curating COBRA Models of Microbial Metabolism.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels.The ISME journal · 2021Article
- Reconstructing organisms in silico: genome-scale models and their emerging applications.Nature reviews. Microbiology · 2020Review
172 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
2 authors.
Funding
Abstract
The number and scope of methods developed to interrogate and use metabolic network reconstructions has significantly expanded over the past 15 years. In particular, Escherichia coli metabolic network reconstruction has reached the genome scale and been utilized to address a broad spectrum of basic and practical applications in five main categories: metabolic engineering, model-directed discovery, interpretations of phenotypic screens, analysis of network properties and studies of evolutionary processes. Spurred on by these accomplishments, the field is expected to move forward and further broaden the scope and content of network reconstructions, develop new and novel in silico analysis tools, and expand in adaptation to uses of proximal and distal causation in biology. Taken together, these efforts will solidify a mechanistic genotype-phenotype relationship for microbial metabolism.
Indexed as
Identifiers
What OpenQuestion holds
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.