ArticleGenome biology2012
MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed.
- Hypergraph learning with multi-dimensional metabolite feature extractions and static-dynamic attention mechanisms to fill missing reactions in metabolic networks.Briefings in bioinformatics · 2026Article
- Design and Analysis of Macroalgae-Based Biorefineries.Methods in molecular biology (Clifton, N.J.) · 2026Article
- MACAW: a method for semi-automatic detection of errors in genome-scale metabolic models.Genome biology · 2025Article
- A dual-scale fused hypergraph convolution-based hyperedge prediction model for predicting missing reactions in genome-scale metabolic networks.Briefings in bioinformatics · 2024Article
- Teasing out missing reactions in genome-scale metabolic networks through hypergraph learning.Nature communications · 2023Article
- Network Reconstruction and Modelling Made Reproducible with moped.Metabolites · 2022Article
- A gap-filling algorithm for prediction of metabolic interactions in microbial communities.PLoS computational biology · 2021Article
- Stoichiometric Modeling of Artificial String Chemistries Reveals Constraints on Metabolic Network Structure.Journal of molecular evolution · 2021Article
- Addressing uncertainty in genome-scale metabolic model reconstruction and analysis.Genome biology · 2021Review
- Systematically gap-filling the genome-scale metabolic model of CHO cells.Biotechnology letters · 2021Article
- Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species.eLife · 2020Article
- Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models.Bioinformatics (Oxford, England) · 2020Article
- ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species.Frontiers in molecular biosciences · 2020Article
- Distributed flux balance analysis simulations of serial biomass fermentation by two organisms.PloS one · 2020Article
- New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering.Frontiers in bioengineering and biotechnology · 2019Review
- Genome-wide analysis of fitness data and its application to improve metabolic models.BMC bioinformatics · 2018Article
- How accurate is automated gap filling of metabolic models?BMC systems biology · 2018Article
- Evaluation of reaction gap-filling accuracy by randomization.BMC bioinformatics · 2018Article
- Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3).PloS one · 2018Article
- Model-enabled gene search (MEGS) allows fast and direct discovery of enzymatic and transport gene functions in the marine bacteriumThe Journal of biological chemistry · 2017Article
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2 authors.
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Abstract
Genome-scale metabolic network reconstructions are considered a key step in quantifying the genotype-phenotype relationship. We present a novel gap-filling approach, MetabolIc Reconstruction via functionAl GEnomics (MIRAGE), which identifies missing network reactions by integrating metabolic flux analysis and functional genomics data. MIRAGE's performance is demonstrated on the reconstruction of metabolic network models of E. coli and Synechocystis sp. and validated via existing networks for these species. Then, it is applied to reconstruct genome-scale metabolic network models for 36 sequenced cyanobacteria amenable for constraint-based modeling analysis and specifically for metabolic engineering. The reconstructed network models are supplied via standard SBML files.
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