ArticleNucleic acids research2015
Reconstructing genome-scale metabolic models with merlin.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers, 1 of them a synthesis that pooled it.
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Who cites it
63 citing papers in PubMed, 1 synthesis or guideline pooled it, 144 citations in OpenAlex.
- Preclinical techniques to investigate exercise training in vascular pathophysiology.American journal of physiology. Heart and circulatory physiology · 2021Pooled it
- Nutrient control enables metabolic reconstruction ofbioRxiv : the preprint server for biology · 2026Article
- High-throughput generation and comparison of genome-scale metabolic models reveal strain-specific metabolic diversity in 439mSystems · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Constraint-Based Metabolic Modeling Approach for Microbial Communities.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Evaluating Metabolic Support in Pairwise Microbial Communities Using MetQuest.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.eLife · 2025Article
- Moving from genome-scale to community-scale metabolic models for the human gut microbiome.Nature microbiology · 2025Review
- Metabolic modeling of host-microbe interactions.Computational and structural biotechnology journal · 2025Review
- Unveiling new features of the human pathogenComputational and structural biotechnology journal · 2025Article
- A diel multi-tissue genome-scale metabolic model of Vitis vinifera.PLoS computational biology · 2024Article
- Genome-resolved metagenomics: a game changer for microbiome medicine.Experimental & molecular medicine · 2024Review
- Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations.Briefings in bioinformatics · 2023Review
- An automated model annotation system (AMAS) for SBML models.Bioinformatics (Oxford, England) · 2023Article
- The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber.PLoS computational biology · 2023Article
- Uses of Multi-Objective Flux Analysis for Optimization of Microbial Production of Secondary Metabolites.Microorganisms · 2023Review
- Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling.Bioinformatics (Oxford, England) · 2023Article
- Machine Learning and Hybrid Methods for Metabolic Pathway Modeling.Methods in molecular biology (Clifton, N.J.) · 2023Review
- Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool.Journal of integrative bioinformatics · 2022Article
- Genome-scale metabolic network models: from first-generation to next-generation.Applied microbiology and biotechnology · 2022Review
3 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 at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Metabolic Models Reconstruction Using Genome-Scale Information (merlin) tool is a user-friendly Java application that aids the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs the major steps of the reconstruction process, including the functional genomic annotation of the whole genome and subsequent construction of the portfolio of reactions. Moreover, merlin includes tools for the identification and annotation of genes encoding transport proteins, generating the transport reactions for those carriers. It also performs the compartmentalisation of the model, predicting the organelle localisation of the proteins encoded in the genome and thus the localisation of the metabolites involved in the reactions promoted by such enzymes. The gene-proteins-reactions (GPR) associations are automatically generated and included in the model. Finally, merlin expedites the transition from genomic data to draft metabolic models reconstructions exported in the SBML standard format, allowing the user to have a preliminary view of the biochemical network, which can be manually curated within the environment provided by merlin.
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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.