ArticleViruses2016
HostPhinder: A Phage Host Prediction Tool.
Article in Viruses, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers, 2 of them syntheses that pooled it.
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Who cites it
95 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
- Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes using machine learning.Nature microbiology · 2026Article
- Innovative Applications of Artificial Intelligence in Bacteriophage Research: A New Chapter in Future Medicine.Microorganisms · 2026Review
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- Ec_Ou_ZC1, a new Tunavirus, reveals Cor superinfection exclusion and differential Avs susceptibility across Drexlerviridae subfamilies.BMC microbiology · 2026Article
- Identifying host-specific patterns in viral protein sequences to predict host spillover risk in animal and plant kingdoms.Scientific reports · 2026Article
- Genomic insights into phage SGP007 reveal a potent therapeutic candidate for targeted control of salmonellosis in poultry.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Phage Frontiers: Genomic and Functional Profiling of Novel Virulent Agents Targeting FoodborneBiology · 2026Article
- PhageCGRNet: Integrating Chaos Game Representation of Genomes with Convolutional Neural Network for accurate phage host classification prediction.PLoS computational biology · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- High-resolution phage-host assignment through key proteins using large language models.Nature communications · 2026Article
- Isolation and Characterization of the Polyvalent Enterobacteria-Infecting Phage Cit2 with Potential for Biocontrol Applications.ACS omega · 2026Article
- Gut virome dynamics: from commensal to critical player in health and disease.Nature reviews. Gastroenterology & hepatology · 2026Review
- Bacteriophages in gut metagenomes: from analysis to application.Virology journal · 2026Review
- The Role of Genomics in Advancing and Standardising Bacteriophage Therapy.Antibiotics (Basel, Switzerland) · 2026Review
- A comprehensive review of AI innovations for tackling antimicrobial resistance.Le infezioni in medicina · 2026Review
- Computational Microbial and Viral Ecology Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- FusionPHI: A phage-host interaction prediction network model based on attention-driven multi-modal feature fusion.PloS one · 2026Article
- PBIP: a deep learning framework for predicting phage-bacterium interactions at the strain level.Briefings in bioinformatics · 2025Article
35 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput approaches for phage characterization within reach. Here, we present HostPhinder, a tool aimed at predicting the bacterial host of phages by examining the phage genome sequence. Using a reference database of 2196 phages with known hosts, HostPhinder predicts the host species of a query phage as the host of the most genomically similar reference phages. As a measure of genomic similarity the number of co-occurring k-mers (DNA sequences of length k) is used. Using an independent evaluation set, HostPhinder was able to correctly predict host genus and species for 81% and 74% of the phages respectively, giving predictions for more phages than BLAST and significantly outperforming BLAST on phages for which both had predictions. HostPhinder predictions on phage draft genomes from the INTESTI phage cocktail corresponded well with the advertised targets of the cocktail. Our study indicates that for most phages genomic similarity correlates well with related bacterial hosts. HostPhinder is available as an interactive web service [1] and as a stand alone download from the Docker registry [2].
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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.