ArticleBioinformatics advances2023
PhaBOX: a web server for identifying and characterizing phage contigs in metagenomic data.
Article in Bioinformatics advances, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers, 3 of them syntheses that pooled it.
What it found
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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.
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Who cites it
89 citing papers in PubMed, 3 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
- Pooled it
- Integrative metagenomic analysis reveals distinct gut microbial signatures related to obesity.BMC microbiology · 2024Pooled it
- The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission.Nature communications · 2024Trial
- Sex- and Time-Resolved Physiological and Gut Ecosystem Responses to a Food-Grade Microbiome-Targeted Intervention in Collegiate Endurance Athletes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Characterization and genomic analysis of a jumbo Aeromonas hydrophila phage BMBAH1, representing a candidate novel viral genus.Virus research · 2026Article
- Extensive horizontal gene transfer drives microbial adaptation and diversification in Kermadec Trench hadal microbiomes.Nature communications · 2026Article
- Genomic and phenotypic characterization of Klebsiella pneumoniae phage KP Ø1: a novel lytic Slopekvirus targeting uropathogenic multidrug-resistant Klebsiella pneumoniae.Scientific reports · 2026Article
- 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
- Article
- Characterization ofMicrobiology spectrum · 2026Article
- Insights Gained by High-throughput Chromosome Conformation Capture (Hi-C) into the Viral Modulation of Methane Production in Anaerobic Digestion.Environmental science & technology · 2026Article
- PhaBOX2: an enhanced web server for discovering and analyzing viral contigs in metagenomic data.Nucleic acids research · 2026Article
- Genome sequence ofMicrobiology resource announcements · 2026Article
- Global long-term agricultural experiments reveal consequences of mineral fertilization for soil microbiomes.Nature communications · 2026Article
- A polyvalent phage shapes bacterial dynamics.Journal of virology · 2026Article
- Comparison and correlation of in vitro and in vivo approaches for determining Pseudomonas aeruginosa bacteriophages activity.BMC microbiology · 2026Article
- Evolutionary interplay: virulence, endolysin-like hydrolases, and defense correlations in the Erwinia amylovora pangenome.BMC microbiology · 2026Article
- CApEsid biOfilm: a suggested pipeline for clinical phage microbiology for biofilm infections based on comparative method study.Scientific reports · 2026Article
29 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
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: There is accumulating evidence showing the important roles of bacteriophages (phages) in regulating the structure and functions of the microbiome. However, lacking an easy-to-use and integrated phage analysis software hampers microbiome-related research from incorporating phages in the analysis. Results: In this work, we developed a web server, PhaBOX, which can comprehensively identify and analyze phage contigs in metagenomic data. It supports integrated phage analysis, including phage contig identification from the metagenomic assembly, lifestyle prediction, taxonomic classification, and host prediction. Instead of treating the algorithms as a black box, PhaBOX also supports visualization of the essential features for making predictions. The web server is designed with a user-friendly graphical interface that enables both informatics-trained and nonspecialist users to analyze phages in microbiome data with ease. Availability and implementation: The web server of PhaBOX is available via: https://phage.ee.cityu.edu.hk. The source code of PhaBOX is available at: https://github.com/KennthShang/PhaBOX.
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.