ArticleGigaScience2021
DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach.
Article in GigaScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
61 citing papers in PubMed, 1 synthesis or guideline pooled it, 99 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
- Research progress on nanomaterials in promoting phage function and application.Applied and environmental microbiology · 2026Review
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- Characterization and antibacterial efficacy of the broad-host-range phage P108 against biofilm-forming and methicillin-resistant Staphylococcus aureus.Virus research · 2026Article
- Review
- Article
- Alterations in the gut virome of children with allergic rhinitis: enrichment of pro-inflammatory bacteriophages and depletion of fungal viruses.Microbiology spectrum · 2026Article
- Phages drive the dissemination of antibiotic resistance genes by facilitating host adaptation to heavy metal stress.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Prophage: agent provocateur?Archives of microbiology · 2026Review
- A Century-Old Solution for 21st Century Challenges: Current Applications with a Focus on Biocontrol, Environmental Impacts, and Regulatory Perspectives.Antibiotics (Basel, Switzerland) · 2026Review
- Elevated temperature simulating heatwaves restructures active nitrifying communities and associated viruses in tidal flats and agricultural soils.The ISME journal · 2026Article
- Metagenomic analysis of the DNA virome communities in swine lungs.Frontiers in microbiology · 2026Article
- Characterization of phage AbpL with a terminally redundant genome and its therapeutic potential against drug-resistantFrontiers in cellular and infection microbiology · 2026Article
- Phages Shape the Transformation of Organic Matter During Composting.Microbial biotechnology · 2025Article
- Characterization of a novel Jumbo phage JP4 with potential to control pathogenic Escherichia coli.Virology journal · 2025Article
- Biogeography and host interactions of CPR and DPANN viruses in acid mine drainage sediments.Nature communications · 2025Article
- Combined pesticide pollution enhances the dissemination of the phage-encoded antibiotic resistome in the soil under nitrogen deposition.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Eco-evolutionary strategies drive viral diversification in nutrient-poor soils across elevation gradients.National science review · 2025Article
- Metagenomic Analysis of the Gastrointestinal Phageome and Incorporated Dysbiosis in Children with Persistent Diarrhea of Unknown Etiology in Vietnam.Pathogens (Basel, Switzerland) · 2025Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundProkaryotic viruses referred to as phages can be divided into virulent and temperate phages. Distinguishing virulent and temperate phage-derived sequences in metavirome data is important for elucidating their different roles in interactions with bacterial hosts and regulation of microbial communities. However, there is no experimental or computational approach to effectively classify their sequences in culture-independent metavirome. We present a new computational method, DeePhage, which can directly and rapidly judge each read or contig as a virulent or temperate phage-derived fragment.
findingsDeePhage uses a "one-hot" encoding form to represent DNA sequences in detail. Sequence signatures are detected via a convolutional neural network to obtain valuable local features. The accuracy of DeePhage on 5-fold cross-validation reaches as high as 89%, nearly 10% and 30% higher than that of 2 similar tools, PhagePred and PHACTS. On real metavirome, DeePhage correctly predicts the highest proportion of contigs when using BLAST as annotation, without apparent preferences. Besides, DeePhage reduces running time vs PhagePred and PHACTS by 245 and 810 times, respectively, under the same computational configuration. By direct detection of the temperate viral fragments from metagenome and metavirome, we furthermore propose a new strategy to explore phage transformations in the microbial community. The ability to detect such transformations provides us a new insight into the potential treatment for human disease.
conclusionsDeePhage is a novel tool developed to rapidly and efficiently identify 2 kinds of phage fragments especially for metagenomics analysis. DeePhage is freely available via http://cqb.pku.edu.cn/ZhuLab/DeePhage or https://github.com/shufangwu/DeePhage.
Indexed as
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.