ArticlePloS one2013
VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 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
94 citing papers in PubMed, 215 citations in OpenAlex.
- Trial
- VISDB 2.0: A manually curated resource of viral integration sites and their regulatory maps in human diseases.Scientific data · 2026Article
- Challenges in the detection and assembly of virus integration structures in human genomes.Frontiers in oncology · 2026Review
- ELViS: an R package for estimating copy number levels of viral genomic segments at base-resolution.Bioinformatics (Oxford, England) · 2025Article
- Genome integration of human DNA oncoviruses.Journal of virology · 2025Review
- Article
- VITALdb: to select the best viroinformatics tools for a desired virus or application.Briefings in bioinformatics · 2025Article
- Molecular characterization of EBV-associated primary pulmonary lymphoepithelial carcinoma by multiomics analysis.BMC cancer · 2025Article
- Detection of viral contamination in cell lines using ViralCellDetector.Frontiers in microbiology · 2025Article
- Integrated characterization of hepatobiliary tumor organoids provides a potential landscape of pharmacogenomic interactions.Cell reports. Medicine · 2024Article
- Endogenous viral elements: insights into data availability and accessibility.Virus evolution · 2024Article
- AI-enabled pipeline for virus detection, validation, and SNP discovery from next-generation sequencing data.Frontiers in genetics · 2024Article
- VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns.Genomics, proteomics & bioinformatics · 2023Article
- Deep learning for detecting and elucidating human T-cell leukemia virus type 1 integration in the human genome.Patterns (New York, N.Y.) · 2023Article
- Enhanced Viral Metagenomics with Lazypipe 2.Viruses · 2023Article
- The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance.Viruses · 2023Review
- Novel cancer gene discovery using a forward genetic screen in RCAS-PDGFB-driven gliomas.Neuro-oncology · 2023Article
- Multiple HPV integration mode in the cell lines based on long-reads sequencing.Frontiers in microbiology · 2023Article
- hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.International journal of molecular sciences · 2022Article
- Loss of PROTEIN TARGETING TO STARCH 2 has variable effects on starch synthesis across organs and species.Journal of experimental botany · 2022Article
34 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
3 authors at 1 institution in 1 country.
Funding
Abstract
Next generation sequencing (NGS) technologies allow us to explore virus interactions with host genomes that lead to carcinogenesis or other diseases; however, this effort is largely hindered by the dearth of efficient computational tools. Here, we present a new tool, VirusFinder, for the identification of viruses and their integration sites in host genomes using NGS data, including whole transcriptome sequencing (RNA-Seq), whole genome sequencing (WGS), and targeted sequencing data. VirusFinder's unique features include the characterization of insertion loci of virus of arbitrary type in the host genome and high accuracy and computational efficiency as a result of its well-designed pipeline. The source code as well as additional data of VirusFinder is publicly available at http://bioinfo.mc.vanderbilt.edu/VirusFinder/.
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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.