ArticleNucleic acids research2019
Prophage Hunter: an integrative hunting tool for active prophages.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 147 papers, 1 of them a synthesis that pooled it.
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Who cites it
147 citing papers in PubMed, 1 synthesis or guideline pooled it, 240 citations in OpenAlex.
- Precision phage therapy in the AI/ML era: a systematic review of discovery-to-clinical translation evidence.Frontiers in microbiology · 2026Pooled it
- Fast, flexible gene cluster family delineation with IGUA.Nucleic acids research · 2026Article
- Innovative Applications of Artificial Intelligence in Bacteriophage Research: A New Chapter in Future Medicine.Microorganisms · 2026Review
- Research on Prophages in Aquaculture from the Perspective of Paradigm Borrowing: Advances in Pathogen Virulence, Antimicrobial Resistance, and Environmental Regulation.Microorganisms · 2026Review
- High-quality phage assembly from metagenomes with PALACE.Nature biotechnology · 2026Article
- Recombination, mobile genetic elements, and genetic transfer contribute to the adaptation of Streptococcus uberis causing mastitis.Veterinary research · 2026Article
- Phage satellites induced by virulent phages are mobilized by natural competence leading to phage resistance in a new host.Nature communications · 2026Article
- Genome-wide comparative and taxonomic characterization of prophages in Stenotrophomonas maltophilia.Archives of microbiology · 2026Article
- High-resolution phage-host assignment through key proteins using large language models.Nature communications · 2026Article
- The hidden role of rhizospheric viruses in promoting nitrogen fixation in soils.Nature communications · 2026Article
- Advances in Shotgun Metagenomics for Cheese Microbiology: From Microbial Dynamics to Functional Insights.Foods (Basel, Switzerland) · 2026Review
- The antagonistic coevolution between Pseudomonas sivasensis W-6 and the cold-adapted phage VW6S.Antonie van Leeuwenhoek · 2026Article
- Targeting Horizontal Gene Transfer to Combat Antimicrobial Resistance: A Review of Mechanisms, Drivers, and Multi-Omics Strategies.Infection and drug resistance · 2026Review
- TattleTail: A Rule-Based Tool for Identifying Canonical Pyocin-Encoding Gene Clusters inComputational and structural biotechnology journal · 2026Article
- Whole-genome sequencing to explore genomic profile, pathogenicity, virulence motifs, and pangenome of clinical MRSA isolates.Scientific reports · 2025Article
- Natural competence in the bacterial pathogen Xylella fastidiosa varies across genotypes and is associated with adhesins.PLoS pathogens · 2025Article
- Prophage Activation: An In Silico Platform for Identifying Prophage Regulatory Elements to Inform Phage Engineering Against Drug-Resistant Bacteria.Life (Basel, Switzerland) · 2025Article
- The genetic diversity and populational specificity of the human gut virome at single-nucleotide resolution.Microbiome · 2025Article
- Molecular and genomic insights into multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa causing burn wound infections in Bangladesh.Scientific reports · 2025Article
- Article
87 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
15 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identifying active prophages is critical for studying coevolution of phage and bacteria, investigating phage physiology and biochemistry, and engineering designer phages for diverse applications. We present Prophage Hunter, a tool aimed at hunting for active prophages from whole genome assembly of bacteria. Combining sequence similarity-based matching and genetic features-based machine learning classification, we developed a novel scoring system that exhibits higher accuracy than current tools in predicting active prophages on the validation datasets. The option of skipping similarity matching is also available so that there's higher chance for novel phages to be discovered. Prophage Hunter provides a one-stop web service to extract prophage genomes from bacterial genomes, evaluate the activity of the prophages, identify phylogenetically related phages, and annotate the function of phage proteins. Prophage Hunter is freely available at https://pro-hunter.bgi.com/.
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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.