ArticleNature biotechnology2025
Machine learning enables scalable and systematic hierarchical virus taxonomy.
Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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Who cites it
20 citing papers in PubMed.
- Virome DNA stable isotope probing reveals diverse active soil virus communities across ecosystem contexts.mSystems · 2026Article
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- Hawaiian geothermal fumaroles contain diverse and novel viruses.Microbiology spectrum · 2026Article
- Longitudinal dynamics of the maternal gut virome associate with metabolic features of preterm birth.Nature communications · 2026Article
- Competing Inter-Domain Quorum-Sensing Systems Control Prophage Lysis-Lysogeny Decisions.bioRxiv : the preprint server for biology · 2026Article
- Metagenomic Analysis of Rural Groundwater Viromes Reveals Bacteriophage Contributions to Groundwater Microbial Ecology.Microbial ecology · 2026Article
- Isolation and characterization of novel bacteriophage, vB_AbaA_SWMUZ8, targeting multidrug-resistant Acinetobacter baumannii strains.BMC microbiology · 2026Article
- The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome.Nature communications · 2026Article
- Virus taxonomy and the ICTV - 21 FAQs for the perplexed virologist.The Journal of general virology · 2026Review
- Environmental disturbances and cyanobacterial traits shape prokaryotic dynamics in a eutrophic Mediterranean coastal lagoon.Environmental microbiome · 2026Article
- Hawaiian Geothermal Fumaroles Contain Diverse and Novel Viruses.bioRxiv : the preprint server for biology · 2026Article
- The chicken gut virome: spatial structuring and extensive diversity of 19,778 viral populations.mSystems · 2026Article
- SS-VIME: a single-source virome-microbiome extraction protocol toward comprehensive soil community analysis.Microbiology spectrum · 2026Article
- Diversity and ecological roles of hidden viral players in groundwater microbiomes.Nature communications · 2026Article
- Isolation and characterization of TayeBlu, a novel bacteriophage ofMicrobiology spectrum · 2026Article
- vClassifier: a toolkit for high-resolution phylogenetic classification of prokaryotic viruses.Bioinformatics advances · 2026Article
- ViTax-RAG: a retrieval-augmented language modeling tool for viral contig taxonomic classification.Bioinformatics advances · 2026Article
- Unraveling the diversity, function, and virus-host interactions of archaeal proviruses.ISME communications · 2026Article
- We need to talk about the virome.Microbiome research reports · 2026Article
- Ecology of prokaryotic DNA viruses in a highly impacted coastal lagoon revealed through comparative and temporal metagenomics.ISME communications · 2026Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Although virus ecogenomics has expanded access to and understanding of the virosphere, existing classification tools lack taxonomic resolution and are unable to scale to modern discovery-based datasets or classify previously unknown sequence space. Here we develop vConTACT3-a machine learning-based tool that improves scalability and accuracy of virus taxonomy. By optimizing gene-sharing thresholds and leveraging adaptive, realm-specific cut-offs, vConTACT3 expands classification to both eukaryote and prokaryote viruses for four of the six officially recognized realms, and establishes accurate hierarchical taxonomy from genus to order. Specifically, vConTACT3 achieves >95% agreement with official taxonomy for 35,545 and 13,524 public prokaryotic and eukaryotic virus genomes, respectively, to surpass vConTACT2 across most realms, while still uniquely classifying previously uncharacterized taxa, and doing so even faster. vConTACT3 application provides taxonomy assignments for tens of thousands of unclassified taxa rapidly, automatically and systematically; evaluates virus sequence space to reveal support for fewer taxonomic ranks than currently available and identifies taxonomically challenging areas across the virosphere.
Identifiers
41420049What OpenQuestion holds
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.