ArticleBioinformatics (Oxford, England)2021
VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Examination of HLA-DRB1*15-linked Candidate Antigens in Still Disease With and Without Lung Disease and Drug-Associated Immune Reactions.The Journal of rheumatology · 2026Article
- Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes.Nature biotechnology · 2026Article
- Host Genetic Architecture between Epstein-Barr Virus Activity and Multiple Sclerosis Reveals Shared Pathways.medRxiv : the preprint server for health sciences · 2025Article
- Association of viral RNAs in the choroid plexus with bipolar disorder and schizophrenia and evidence for the hepatitis C virus involvement in neuropathology.Translational psychiatry · 2025Article
- A survey of pathogenic involvement in non-communicable human diseases.Communications medicine · 2025Article
- Higher Expression of HPV16 Derived E7_LI Transcript Observed in Men With HIV and Recurrent Anal Cancer.Journal of medical virology · 2025Article
- Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression.bioRxiv : the preprint server for biology · 2025Article
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- Multi-Omic Data Integration Suggests Putative Microbial Drivers of Aetiopathogenesis in Mycosis Fungoides.Cancers · 2024Article
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- Genomic landscape of glioblastoma without IDH somatic mutation in 42 cases: a comprehensive analysis using RNA sequencing data.Journal of neuro-oncology · 2024Article
- Lack of strong innate immune reactivity renders macrophages alone unable to control productive Varicella-Zoster Virus infection in an isogenic human iPSC-derived neuronal co-culture model.Frontiers in immunology · 2023Article
- Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data.PLoS computational biology · 2022Article
- Myasthenia gravis-specific aberrant neuromuscular gene expression by medullary thymic epithelial cells in thymoma.Nature communications · 2022Article
- MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data.Briefings in bioinformatics · 2022Article
- Whole-transcriptome sequencing-based concomitant detection of viral and human genetic determinants of cutaneous lesions.JCI insight · 2022Article
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Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryThe possibility that RNA transcripts from clinical samples contain plenty of virus RNAs has not been pursued actively so far. We here developed a new tool for analyzing virus-transcribed mRNAs, not virus copy numbers, in the data of bulk and single-cell RNA-sequencing of human cells. Our pipeline, named VIRTUS (VIRal Transcript Usage Sensor), was able to detect 762 viruses including herpesviruses, retroviruses and even SARS-CoV-2 (COVID-19), and quantify their transcripts in the sequence data. This tool thus enabled simultaneously detecting infected cells, the composition of multiple viruses within the cell, and the endogenous host-gene expression profile of the cell. This bioinformatics method would be instrumental in addressing the possible effects of covertly infecting viruses on certain diseases and developing new treatments to target such viruses. AVAILABILITY AND IMPLEMENTATION: : VIRTUS is implemented using Common Workflow Language and Docker under a CC-NC license. VIRTUS is freely available at https://github.com/yyoshiaki/VIRTUS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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