ArticleScientific reports2018
Discovering viral genomes in human metagenomic data by predicting unknown protein families.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 17 citations in OpenAlex.
- Article
- Genetic Diversity and Genomic Characteristics of the Respiratory Virome in Patients With Severe Fungal Infections.Journal of medical virology · 2026Article
- Gut Virome: What's the Role in Irritable Bowel Syndrome?Reviews in medical virology · 2025Review
- Gut Virome and Aging: Phage-Driven Microbial Stability and Immune Modulation.Aging and disease · 2025Review
- Review
- Charting Peptide Shared Sequences Between 'Diabetes-Viruses' and Human Pancreatic Proteins, Their Structural and Autoimmune Implications.Bioinformatics and biology insights · 2024Article
- Post-genomic platform for development of oligonucleotide vaccines against RNA viruses: diamond cuts diamond.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2022Article
- Metagenomic profiling of placental tissue suggests DNA virus infection of the placenta is rare.The Journal of general virology · 2021Article
- Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths.Microorganisms · 2020Review
- The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View.Trends in cancer · 2020Review
- Short k-mer abundance profiles yield robust machine learning features and accurate classifiers for RNA viruses.PloS one · 2020Article
- Gut virome of mammals and birds reveals high genetic diversity of the familyVirus evolution · 2019Article
- Genetic and functional diversity of double-stranded DNA viruses in a tropical monsoonal estuary, India.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Massive amounts of metagenomics data are currently being produced, and in all such projects a sizeable fraction of the resulting data shows no or little homology to known sequences. It is likely that this fraction contains novel viruses, but identification is challenging since they frequently lack homology to known viruses. To overcome this problem, we developed a strategy to detect ORFan protein families in shotgun metagenomics data, using similarity-based clustering and a set of filters to extract bona fide protein families. We applied this method to 17 virus-enriched libraries originating from human nasopharyngeal aspirates, serum, feces, and cerebrospinal fluid samples. This resulted in 32 predicted putative novel gene families. Some families showed detectable homology to sequences in metagenomics datasets and protein databases after reannotation. Notably, one predicted family matches an ORF from the highly variable Torque Teno virus (TTV). Furthermore, follow-up from a predicted ORFan resulted in the complete reconstruction of a novel circular genome. Its organisation suggests that it most likely corresponds to a novel bacteriophage in the microviridae family, hence it was named bacteriophage HFM.
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