ArticleGenome biology2021
gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 183 papers, 1 of them a synthesis that pooled it.
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Who cites it
183 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A gut microbial signature for combination immune checkpoint blockade across cancer types.Nature medicine · 2024Pooled it
- Trial
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- The Biotechnological Applications of Marine Bacteria.Biology · 2026Review
- BioEMMA: Automated Generation of Model-Specific Escher-Compatible Maps from KEGG Pathways.Biology · 2026Article
- Loss of TGR5-activating bile acids is associated with disease activity in inflammatory bowel disease.Scientific reports · 2026Article
- AlphaGEM enables precise genome-scale metabolic modelling by integrating protein structure alignment with deep-learning-based dark metabolism mining.Nature communications · 2026Article
- In silico metabolic profiling of non-baumannii Acinetobacter species uncovers conserved functions and provides first evidence of siderophore biosynthetic genes in Acinetobacter junii.Scientific reports · 2026Article
- Genomic analysis identifies candidate SOS-associated and EPS/envelope-remodeling islands in a drinking-water Stenotrophomonas maltophilia complex isolate.Scientific reports · 2026Article
- Nutrient control enables metabolic reconstruction ofbioRxiv : the preprint server for biology · 2026Article
- Multi-omics characterization of the skin microbiota reveals the anti-aging roles of Stenotrophomonas maltophilia.Microbiome · 2026Article
- Ecological and metabolic restructuring of anaerobic microbiomes under sulfate stress via magnetite-enhanced cooperative networks.Microbiome · 2026Article
- Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome.Nature communications · 2026Article
- Ammonia oxidation and recalcitrant carbon degradation fuel mixotrophic growth in the symbiont community of a deep-sea sponge.Microbiome · 2026Article
- Selecting methods for draft GEM generation in multicellular eukaryotes: a comparative analysis.BMC bioinformatics · 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
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- A Novel Topology-Based Candidate Reaction Prediction Approach for Gap-Fillings of Genome-Scale Metabolic Models.Metabolites · 2026Article
123 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-scale metabolic models of microorganisms are powerful frameworks to predict phenotypes from an organism's genotype. While manual reconstructions are laborious, automated reconstructions often fail to recapitulate known metabolic processes. Here we present gapseq ( https://github.com/jotech/gapseq ), a new tool to predict metabolic pathways and automatically reconstruct microbial metabolic models using a curated reaction database and a novel gap-filling algorithm. On the basis of scientific literature and experimental data for 14,931 bacterial phenotypes, we demonstrate that gapseq outperforms state-of-the-art tools in predicting enzyme activity, carbon source utilisation, fermentation products, and metabolic interactions within microbial communities.
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