ArticleScientific reports2019
Host Taxon Predictor - A Tool for Predicting Taxon of the Host of a Newly Discovered Virus.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Precision phage therapy in the AI/ML era: a systematic review of discovery-to-clinical translation evidence.Frontiers in microbiology · 2026Pooled it
- Identifying host-specific patterns in viral protein sequences to predict host spillover risk in animal and plant kingdoms.Scientific reports · 2026Article
- HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification.GigaScience · 2026Article
- The association of the rumen virome with methane emissions in dairy cattle.Communications biology · 2025Article
- The effect of taxonomic, host-dependent features and sample bias on virus host prediction using machine learning and short sequence k-mers.Scientific reports · 2025Article
- Role of nucleotide pair frequency and synonymous codon usage in the evolution of bovine viral diarrhea virus.Archives of virology · 2025Article
- IPEV: identification of prokaryotic and eukaryotic virus-derived sequences in virome using deep learning.GigaScience · 2024Article
- PacBio sequencing of human fecal samples uncovers the DNA methylation landscape of 22 673 gut phages.Nucleic acids research · 2023Article
- Using machine learning to detect coronaviruses potentially infectious to humans.Scientific reports · 2023Article
- Classification of Highly Divergent Viruses from DNA/RNA Sequence Using Transformer-Based Models.Biomedicines · 2023Article
- iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria.PLoS biology · 2023Article
- Bioinformatics approaches for unveiling virus-host interactions.Computational and structural biotechnology journal · 2023Review
- Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome.PloS one · 2023Article
- Computational Tools for the Analysis of Uncultivated Phage Genomes.Microbiology and molecular biology reviews : MMBR · 2022Review
- Computational Prediction of Bacteriophage Host Ranges.Microorganisms · 2022Review
- DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach.GigaScience · 2021Article
- Predicting hosts based on early SARS-CoV-2 samples and analyzing the 2020 pandemic.Scientific reports · 2021Article
- Interpretable detection of novel human viruses from genome sequencing data.NAR genomics and bioinformatics · 2021Article
- Predicting host taxonomic information from viral genomes: A comparison of feature representations.PLoS computational biology · 2020Article
- Computational approaches in viral ecology.Computational and structural biotechnology journal · 2020Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in metagenomics provided a valuable alternative to culture-based approaches for better sampling viral diversity. However, some of newly identified viruses lack sequence similarity to any of previously sequenced ones, and cannot be easily assigned to their hosts. Here we present a bioinformatic approach to this problem. We developed classifiers capable of distinguishing eukaryotic viruses from the phages achieving almost 95% prediction accuracy. The classifiers are wrapped in Host Taxon Predictor (HTP) software written in Python which is freely available at https://github.com/wojciech-galan/viruses_classifier . HTP's performance was later demonstrated on a collection of newly identified viral genomes and genome fragments. In summary, HTP is a culture- and alignment-free approach for distinction between phages and eukaryotic viruses. We have also shown that it is possible to further extend our method to go up the evolutionary tree and predict whether a virus can infect narrower taxa.
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