ArticleViruses2021
Informative Regions In Viral Genomes.
Article in Viruses, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed, 24 citations in OpenAlex.
- Long-term health outcomes in adolescents with obesity treated with faecal microbiota transplantation: 4-year follow-up.Nature communications · 2025Trial
- Fecal microbiota transplantation alters gut phage communities in a clinical trial for obesity.Microbiome · 2024Trial
- Phage-mediated horizontal transfer ofiMeta · 2025Article
- First detection of a lizard-associated papillomavirus in the splendid japalure (Frontiers in microbiology · 2025Article
- Fine-tuning protein language models unlocks the potential of underrepresented viral proteomes.PeerJ · 2025Article
- Soil viral-host interactions regulate microplastic-dependent carbon storage.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology.Microbiome · 2024Article
- Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants.GigaScience · 2024Article
- Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology.bioRxiv : the preprint server for biology · 2023Article
- VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models.PLoS computational biology · 2023Article
- Deciphering Phage-Host Specificity Based on the Association of Phage Depolymerases and Bacterial Surface Glycan with Deep Learning.bioRxiv : the preprint server for biology · 2023Article
- Article
- Biological foundations of successful bacteriophage therapy.EMBO molecular medicine · 2022Review
- Computational Tools for the Analysis of Uncultivated Phage Genomes.Microbiology and molecular biology reviews : MMBR · 2022Review
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 at 1 institution in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viruses, far from being just parasites affecting hosts' fitness, are major players in any microbial ecosystem. In spite of their broad abundance, viruses, in particular bacteriophages, remain largely unknown since only about 20% of sequences obtained from viral community DNA surveys could be annotated by comparison with public databases. In order to shed some light into this genetic dark matter we expanded the search of orthologous groups as potential markers to viral taxonomy from bacteriophages and included eukaryotic viruses, establishing a set of 31,150 ViPhOGs (Eukaryotic Viruses and Phages Orthologous Groups). To do this, we examine the non-redundant viral diversity stored in public databases, predict proteins in genomes lacking such information, and used all annotated and predicted proteins to identify potential protein domains. The clustering of domains and unannotated regions into orthologous groups was done using cogSoft. Finally, we employed a random forest implementation to classify genomes into their taxonomy and found that the presence or absence of ViPhOGs is significantly associated with their taxonomy. Furthermore, we established a set of 1457 ViPhOGs that given their importance for the classification could be considered as markers or signatures for the different taxonomic groups defined by the ICTV at the order, family, and genus levels.
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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.