ArticleNucleic acids research2017
Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 178 papers, 2 of them syntheses that pooled it.
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Who cites it
178 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- From genomic signals to prediction tools: a critical feature analysis and rigorous benchmark for phage-host prediction.Briefings in bioinformatics · 2025Pooled it
- Advances in phage-host interaction prediction: in silico method enhances the development of phage therapies.Briefings in bioinformatics · 2024Pooled it
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- Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.Science advances · 2026Article
- DNA viruses are constrained to ecological niches and share similar environmental adaptations with hosts.Nature communications · 2026Article
- Review
- Identifying host-specific patterns in viral protein sequences to predict host spillover risk in animal and plant kingdoms.Scientific reports · 2026Article
- The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome.Nature communications · 2026Article
- The chicken gut virome: spatial structuring and extensive diversity of 19,778 viral populations.mSystems · 2026Article
- Hi-C Links Reveal Viral Activity and Infection Within the Free-Living Microbial Community of a Secondary Chlorophyll Maximum in the Eastern Tropical North Pacific.Environmental microbiology · 2026Article
- PhageCGRNet: Integrating Chaos Game Representation of Genomes with Convolutional Neural Network for accurate phage host classification prediction.PLoS computational biology · 2026Article
- High-resolution phage-host assignment through key proteins using large language models.Nature communications · 2026Article
- Diversity and ecological potential of sediment viruses from Chinese continental shelf seas.NPJ biofilms and microbiomes · 2026Article
- From structure to design: experimental and AI-driven approaches in receptor-binding protein engineering for reprogramming phage host range.Archives of microbiology · 2026Review
- Article
- FusionPHI: A phage-host interaction prediction network model based on attention-driven multi-modal feature fusion.PloS one · 2026Article
- Artificial Intelligence Applications in Bacteriophage Genomics and Host Interaction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A deep Siamese network framework for precision phage selection in pulmonary infections.Frontiers in medicine · 2026Article
- Artificial Intelligence Applications in Bacteriophage Genomics and Host Interaction.Methods in molecular biology (Clifton, N.J.) · 2026Article
118 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Viruses and their host genomes often share similar oligonucleotide frequency (ONF) patterns, which can be used to predict the host of a given virus by finding the host with the greatest ONF similarity. We comprehensively compared 11 ONF metrics using several k-mer lengths for predicting host taxonomy from among ∼32 000 prokaryotic genomes for 1427 virus isolate genomes whose true hosts are known. The background-subtracting measure [Formula: see text] at k = 6 gave the highest host prediction accuracy (33%, genus level) with reasonable computational times. Requiring a maximum dissimilarity score for making predictions (thresholding) and taking the consensus of the 30 most similar hosts further improved accuracy. Using a previous dataset of 820 bacteriophage and 2699 bacterial genomes, [Formula: see text] host prediction accuracies with thresholding and consensus methods (genus-level: 64%) exceeded previous Euclidian distance ONF (32%) or homology-based (22-62%) methods. When applied to metagenomically-assembled marine SUP05 viruses and the human gut virus crAssphage, [Formula: see text]-based predictions overlapped (i.e. some same, some different) with the previously inferred hosts of these viruses. The extent of overlap improved when only using host genomes or metagenomic contigs from the same habitat or samples as the query viruses. The [Formula: see text] ONF method will greatly improve the characterization of novel, metagenomic viruses.
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