ArticleNAR genomics and bioinformatics2021
Rapid discovery of novel prophages using biological feature engineering and machine learning.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 2 of them syntheses that pooled it.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
43 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Precision phage therapy in the AI/ML era: a systematic review of discovery-to-clinical translation evidence.Frontiers in microbiology · 2026Pooled it
- Antimicrobial resistance crisis: could artificial intelligence be the solution?Military Medical Research · 2024Pooled it
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- LAMBDA: a prophage detection benchmark for genomic language models.NAR genomics and bioinformatics · 2026Article
- Data mining reveals the diversity of prophage endolysins targeting pathogenic enterococci.The Journal of general virology · 2026Article
- Isolation of novel phages from a resistant Dorea longicatena strain reveals genes associated with phage resistance.Npj viruses · 2026Article
- An ancient genome of Streptococcus pyogenes from a pre-Columbian Bolivian mummy.Nature communications · 2026Article
- LAMBDA: A Prophage Detection Benchmark for Genomic Language Models.bioRxiv : the preprint server for biology · 2026Article
- Large-scale analysis of bacterial genomes reveals thousands of lytic phages.Nature microbiology · 2026Article
- Comparative Genomics of Lactococcus spp. From Global Aquaculture Outbreaks Reveals Virulence Determinants, Antibiotic Resistance, and Phage Defence Mechanisms.MicrobiologyOpen · 2025Article
- Protein Set Transformer: a protein-based genome language model to power high-diversity viromics.Nature communications · 2025Article
- Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases.Nature communications · 2025Article
- Characterization of humanMicrobiology resource announcements · 2025Article
- Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world.Briefings in bioinformatics · 2025Review
- Genomic characterization and probiotic assessment of Bifidobacterium breve JKL2022 with strain-specific CLA-converting properties.Scientific reports · 2025Article
- TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses.Science (New York, N.Y.) · 2025Article
- Fully resolved genome assembly of aMicrobiology resource announcements · 2025Article
- The gut virome and human health: From diversity to personalized medicine.Engineering microbiology · 2025Review
- Development of Chimera AMP-Endolysin with Wider Spectra Against Gram-Negative Bacteria Using High-Throughput Assay.Viruses · 2025Article
- Engineering Phages to Fight Multidrug-Resistant Bacteria.Chemical reviews · 2025Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Prophages are phages that are integrated into bacterial genomes and which are key to understanding many aspects of bacterial biology. Their extreme diversity means they are challenging to detect using sequence similarity, yet this remains the paradigm and thus many phages remain unidentified. We present a novel, fast and generalizing machine learning method based on feature space to facilitate novel prophage discovery. To validate the approach, we reanalyzed publicly available marine viromes and single-cell genomes using our feature-based approaches and found consistently more phages than were detected using current state-of-the-art tools while being notably faster. This demonstrates that our approach significantly enhances bacteriophage discovery and thus provides a new starting point for exploring new biologies.
Identifiers
What 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.