ArticleBriefings in bioinformatics2023
PhaTYP: predicting the lifestyle for bacteriophages using BERT.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 papers, 4 of them syntheses that pooled it.
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Who cites it
136 citing papers in PubMed, 4 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
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- Antimicrobial resistance crisis: could artificial intelligence be the solution?Military Medical Research · 2024Pooled it
- Antimicrobial resistance crisis: could artificial intelligence be the solution?Military Medical Research · 2024Pooled it
- Gut virome dysbiosis contributes to premature ovarian insufficiency by modulating gut bacteriome.Gut microbes · 2026Article
- Phage anti-defense genes targeting NADVirulence · 2026Article
- Phage Genomics and Bioinformatics in Therapeutic Development: Evidence Limits, Validation Gates, and Translational Decision-Making.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Dental wastewater reveals a hidden reservoir of oral bacteriophage diversity.Microbiology spectrum · 2026Article
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- Maternal contact and age-dependent succession influence the assembly of the calf rumen microbiome and virome.Microbiology spectrum · 2026Article
- Characterization ofMicrobiology spectrum · 2026Article
- Adaptation of Soil Viruses to Salinity Stress: Insights Into Genome Size Expansion and Functional Diversification.Environmental microbiology · 2026Article
- Significant variability in virulence factors and antibiotic resistance of uropathogenic Escherichia coli strains may be counteracted by their susceptibility to lytic bacteriophages.Scientific reports · 2026Article
- Article
- Host phylogeny and diet shape gut microbiome and virome in wild small mammals of Gongga Mountain, China.Zoological research · 2026Article
- PhaBOX2: an enhanced web server for discovering and analyzing viral contigs in metagenomic data.Nucleic acids research · 2026Article
- Viral modulation of sulfur-oxidizing bacteria drives organic carbon sink formation during primary succession in deglaciating ecosystems.Nature communications · 2026Article
- Metagenomic Analysis of Rural Groundwater Viromes Reveals Bacteriophage Contributions to Groundwater Microbial Ecology.Microbial ecology · 2026Article
- Genome sequence of a lytic phage phi1_171026 targeting carbapenem-resistantMicrobiology resource announcements · 2026Article
- Complete genome sequence of theMicrobiology resource announcements · 2026Article
76 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Bacteriophages (or phages), which infect bacteria, have two distinct lifestyles: virulent and temperate. Predicting the lifestyle of phages helps decipher their interactions with their bacterial hosts, aiding phages' applications in fields such as phage therapy. Because experimental methods for annotating the lifestyle of phages cannot keep pace with the fast accumulation of sequenced phages, computational method for predicting phages' lifestyles has become an attractive alternative. Despite some promising results, computational lifestyle prediction remains difficult because of the limited known annotations and the sheer amount of sequenced phage contigs assembled from metagenomic data. In particular, most of the existing tools cannot precisely predict phages' lifestyles for short contigs. In this work, we develop PhaTYP (Phage TYPe prediction tool) to improve the accuracy of lifestyle prediction on short contigs. We design two different training tasks, self-supervised and fine-tuning tasks, to overcome lifestyle prediction difficulties. We rigorously tested and compared PhaTYP with four state-of-the-art methods: DeePhage, PHACTS, PhagePred and BACPHLIP. The experimental results show that PhaTYP outperforms all these methods and achieves more stable performance on short contigs. In addition, we demonstrated the utility of PhaTYP for analyzing the phage lifestyle on human neonates' gut data. This application shows that PhaTYP is a useful means for studying phages in metagenomic data and helps extend our understanding of microbial communities.
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