ReviewGenome biology2021
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis.
Review in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 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
80 citing papers in PubMed.
- Enzyme kinetics shapes the growth response of metabolic networks.PLoS computational biology · 2026Article
- WASP: a pipeline for functional annotation prediction based on AlphaFold structural models.Nature communications · 2026Article
- Predictive Algal Systems Biology: Integrating Omics, Genome-Scale Metabolic Models, and Machine Learning.Bioengineering (Basel, Switzerland) · 2026Review
- Defining metabolic niches for marine microbial heterotrophs.Science advances · 2026Article
- Systematic data-driven genome-scale metabolic model reduction for bioprocess modeling: CHO culture case study.NPJ systems biology and applications · 2026Article
- A multi-way SMILES-based hypergraph inference network for metabolic model reconstruction.Communications biology · 2026Article
- MCC: automated mass and charge curation at the genome scale applied toMicrobiology spectrum · 2026Article
- Substrate utilization and cross-feeding synergistically determine microbiome resistance to pathogen invasion.Nature ecology & evolution · 2026Article
- A Closed Computational-Experimental Loop Identifies Metabolic Collapse at the Root of Macrophage Dysfunction due to Zinc Dyshomeostasis.bioRxiv : the preprint server for biology · 2026Article
- Article
- A fusion-based multiomics classification approach for enhanced gene discovery in non-small cell lung cancer.Bioinformatics advances · 2026Article
- Viral lysis and host reprogramming impact carbohydrate, amino acid, and osmolyte cycling in salt-marsh tidal creek sediments.ISME communications · 2026Article
- Biophysical metabolic modeling of complex bacterial colony morphology.Cell systems · 2025Article
- Minimization of proteome reallocation explains metabolic transition in hierarchical utilization of carbon sources.mSystems · 2025Article
- A survey of computational approaches for characterizing microbial interactions in microbial mats.Genome biology · 2025Review
- Moving from genome-scale to community-scale metabolic models for the human gut microbiome.Nature microbiology · 2025Review
- Seed2LP: seed inference in metabolic networks for reverse ecology applications.Bioinformatics (Oxford, England) · 2025Article
- Metabolic Objectives and Trade-Offs: Inference and Applications.Metabolites · 2025Review
- In silico encounters: harnessing metabolic modelling to understand plant-microbe interactions.FEMS microbiology reviews · 2025Review
- Collaborative metabolic curation of an emerging model marine bacterium, Alteromonas macleodii ATCC 27126.PloS one · 2025Article
20 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
4 authors.
Funding
Abstract
The reconstruction and analysis of genome-scale metabolic models constitutes a powerful systems biology approach, with applications ranging from basic understanding of genotype-phenotype mapping to solving biomedical and environmental problems. However, the biological insight obtained from these models is limited by multiple heterogeneous sources of uncertainty, which are often difficult to quantify. Here we review the major sources of uncertainty and survey existing approaches developed for representing and addressing them. A unified formal characterization of these uncertainties through probabilistic approaches and ensemble modeling will facilitate convergence towards consistent reconstruction pipelines, improved data integration algorithms, and more accurate assessment of predictive capacity.
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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.