ArticleNature biotechnology2024
Identification of mobile genetic elements with geNomad.
Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 652 papers, 1 of them a synthesis that pooled it.
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Who cites it
652 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A meta-analysis of infant gut viromes reveals global patterns in bacteriophage community assembly and functional capacity over the first three years of life.Nature communications · 2026Pooled it
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- Phage-ICE tandems facilitate bacterial adaptation and antimicrobial resistance spread.Science advances · 2026Article
- Genomic and functional characterization of Bacillus subtilis subsp. subtilis INPA R296 with emulsifying activity in cultivation with residual soybean oil.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Deciphering pervasive domestication and active "dark matter" of proviruses in prokaryotes via precision border mapping.Science advances · 2026Article
- Plasmidomics: studying plasmids as ecological entities beyond their hosts.Microbial genomics · 2026Review
- Characterization of defensome genes and mobile genetic Elements in different types of pasture soil agroecosystems from the Brazilian Amazon.International microbiology : the official journal of the Spanish Society for Microbiology · 2026Article
- Members of theMicrobial genomics · 2026Article
- Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants.Journal of advanced research · 2026Article
- Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes using machine learning.Nature microbiology · 2026Article
- Diversity of Antarctic sea ice and under-ice seawater RNA viruses.Applied and environmental microbiology · 2026Article
- Microbiological safety and antimicrobial resistance in cashew-based plant-based cheese analogues.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Ancestral hydrocarbon metabolism enables PET degradation by a natural bacterial consortium.mSystems · 2026Article
- Virome DNA stable isotope probing reveals diverse active soil virus communities across ecosystem contexts.mSystems · 2026Article
- Genome-wide characterization of host factors involved in single-stranded RNA and DNA phage infection pathways.bioRxiv : the preprint server for biology · 2026Article
592 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological applications and impact on public health. Here we introduce geNomad, a classification and annotation framework that combines information from gene content and a deep neural network to identify sequences of plasmids and viruses. geNomad uses a dataset of more than 200,000 marker protein profiles to provide functional gene annotation and taxonomic assignment of viral genomes. Using a conditional random field model, geNomad also detects proviruses integrated into host genomes with high precision. In benchmarks, geNomad achieved high classification performance for diverse plasmids and viruses (Matthews correlation coefficient of 77.8% and 95.3%, respectively), substantially outperforming other tools. Leveraging geNomad's speed and scalability, we processed over 2.7 trillion base pairs of sequencing data, leading to the discovery of millions of viruses and plasmids that are available through the IMG/VR and IMG/PR databases. geNomad is available at https://portal.nersc.gov/genomad .
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