ArticleeLife2018
A comprehensive and quantitative exploration of thousands of viral genomes.
Article in eLife, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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
49 citing papers in PubMed.
- Neglected kingdoms: the gut virome, mycobiome and their role in inflammatory bowel disease.Gut microbes · 2026Review
- Systematic mapping of bacteriophage gene essentiality with HIDEN-SEQ.Nature microbiology · 2026Article
- LAMBDA: a prophage detection benchmark for genomic language models.NAR genomics and bioinformatics · 2026Article
- LAMBDA: A Prophage Detection Benchmark for Genomic Language Models.bioRxiv : the preprint server for biology · 2026Article
- Basic Virology.Advances in experimental medicine and biology · 2026Review
- A satellite in the phage universe: isolation and characterization of six novelFEMS microbes · 2026Article
- Review
- Evolutionary interplay between viruses and R-loops.FEBS letters · 2025Review
- Computational function prediction of bacteria and phage proteins.Microbiology and molecular biology reviews : MMBR · 2025Review
- Protein Language Models Expose Viral Immune Mimicry.Viruses · 2025Article
- Double-stranded DNA viruses may serve as vectors for horizontal transfer of intron-generating transposons.Mobile DNA · 2025Article
- Bioinformatic Identification of Viral Genomes from High-Throughput Metagenomic Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Fine-tuning protein language models unlocks the potential of underrepresented viral proteomes.PeerJ · 2025Article
- Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium.Scientific reports · 2024Article
- Unveiling the role of host kinases at different steps of influenza A virus life cycle.Journal of virology · 2024Review
- The Interrelationship between HIV Infection and COVID-19: A Review of the Literature.Current HIV research · 2024Review
- Article
- Machine learning models can identify individuals based on a resident oral bacteriophage family.Frontiers in microbiomes · 2024Article
- Adaptation of turnip mosaic virus toVirus evolution · 2024Article
- Phylogenomic analysis expands the known repertoire of single-stranded DNA viruses in benthic zones of the South Indian Ocean.ISME communications · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The complete assembly of viral genomes from metagenomic datasets (short genomic sequences gathered from environmental samples) has proven to be challenging, so there are significant blind spots when we view viral genomes through the lens of metagenomics. One approach to overcoming this problem is to leverage the thousands of complete viral genomes that are publicly available. Here we describe our efforts to assemble a comprehensive resource that provides a quantitative snapshot of viral genomic trends - such as gene density, noncoding percentage, and abundances of functional gene categories - across thousands of viral genomes. We have also developed a coarse-grained method for visualizing viral genome organization for hundreds of genomes at once, and have explored the extent of the overlap between bacterial and bacteriophage gene pools. Existing viral classification systems were developed prior to the sequencing era, so we present our analysis in a way that allows us to assess the utility of the different classification systems for capturing genomic trends.
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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.