ArticlePatterns (New York, N.Y.)2021
RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content.
Article in Patterns (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers, 2 of them syntheses 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
87 citing papers in PubMed, 2 syntheses or guidelines pooled it, 133 citations in OpenAlex.
- From genomic signals to prediction tools: a critical feature analysis and rigorous benchmark for phage-host prediction.Briefings in bioinformatics · 2025Pooled it
- Advances in phage-host interaction prediction: in silico method enhances the development of phage therapies.Briefings in bioinformatics · 2024Pooled it
- Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes using machine learning.Nature microbiology · 2026Article
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- Phage host range: determinants, dynamics and applications.Nature reviews. Microbiology · 2026Review
- Chemical prophage induction selectively removes Vibrio from a pelagic Sargassum-derived multispecies biofilm.Environmental microbiome · 2026Article
- Viral modulation of sulfur-oxidizing bacteria drives organic carbon sink formation during primary succession in deglaciating ecosystems.Nature communications · 2026Article
- Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.Science advances · 2026Article
- DNA viruses are constrained to ecological niches and share similar environmental adaptations with hosts.Nature communications · 2026Article
- Review
- Identifying host-specific patterns in viral protein sequences to predict host spillover risk in animal and plant kingdoms.Scientific reports · 2026Article
- The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome.Nature communications · 2026Article
- The chicken gut virome: spatial structuring and extensive diversity of 19,778 viral populations.mSystems · 2026Article
- Hi-C Links Reveal Viral Activity and Infection Within the Free-Living Microbial Community of a Secondary Chlorophyll Maximum in the Eastern Tropical North Pacific.Environmental microbiology · 2026Article
- PhageCGRNet: Integrating Chaos Game Representation of Genomes with Convolutional Neural Network for accurate phage host classification prediction.PLoS computational biology · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- High-resolution phage-host assignment through key proteins using large language models.Nature communications · 2026Article
- The epidermal ecotone: a proposed model system for marine viral ecology at the animal-environmental interface.NPJ biofilms and microbiomes · 2026Review
- Gut virome dynamics: from commensal to critical player in health and disease.Nature reviews. Gastroenterology & hepatology · 2026Review
- Multi-kingdom fecal microbiome and virus-host interactions associated with growth performance of indigenous beef calves in Guizhou.BMC microbiology · 2026Article
27 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
8 authors at 4 institutions in 5 countries.
Funding
Abstract
Culture-independent approaches have recently shed light on the genomic diversity of viruses of prokaryotes. One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), that uses scores to 43,644 protein clusters to assign hosts to complete or fragmented genomes of viruses of Archaea and Bacteria. RaFAH displayed performance comparable with that of other methods for virus-host prediction in three different benchmarks encompassing viruses from RefSeq, single amplified genomes, and metagenomes. RaFAH was applied to assembled metagenomic datasets of uncultured viruses from eight different biomes of medical, biotechnological, and environmental relevance. Our analyses led to the identification of 537 sequences of archaeal viruses representing unknown lineages, whose genomes encode novel auxiliary metabolic genes, shedding light on how these viruses interfere with the host molecular machinery. RaFAH is available at https://sourceforge.net/projects/rafah/.
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.