ArticleGenome medicine2015
VERSE: a novel approach to detect virus integration in host genomes through reference genome customization.
Article in Genome medicine, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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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.
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Who cites it
47 citing papers in PubMed, 126 citations in OpenAlex.
- Mapping the Heterogeneity of Histone Modifications on Hepatitis B Virus DNA Using Liver Needle Biopsies Obtained from Chronically Infected Patients.Journal of virology · 2019Trial
- VISDB 2.0: A manually curated resource of viral integration sites and their regulatory maps in human diseases.Scientific data · 2026Article
- RAAVioli: A comprehensive approach to characterizing AAV vector integrations and rearrangements.Molecular therapy. Advances · 2026Article
- ELViS: an R package for estimating copy number levels of viral genomic segments at base-resolution.Bioinformatics (Oxford, England) · 2025Article
- The complexity of tobacco smoke-induced mutagenesis in head and neck cancer.Nature genetics · 2025Article
- HPV-KITE: sequence analysis software for rapid HPV genotype detection.Briefings in bioinformatics · 2025Article
- Detection of viral contamination in cell lines using ViralCellDetector.Frontiers in microbiology · 2025Article
- Detection of HBV DNA integration in plasma cell-free DNA of different HBV diseases utilizing DNA capture strategy.Virologica Sinica · 2024Article
- Human papillomavirus integration transforms chromatin to drive oncogenesis.Genome biology · 2023Article
- GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture.Database : the journal of biological databases and curation · 2023Article
- VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns.Genomics, proteomics & bioinformatics · 2023Article
- ViReMa: a virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids.GigaScience · 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
- hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.International journal of molecular sciences · 2022Article
- Article
- HBV genome-enriched single cell sequencing revealed heterogeneity in HBV-driven hepatocellular carcinoma (HCC).BMC medical genomics · 2022Article
- FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA.NAR genomics and bioinformatics · 2022Article
- Genomic characterization of small cell carcinomas of the uterine cervix.Molecular oncology · 2022Article
- Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage.Frontiers in microbiology · 2022Article
- The Effects and Underlying Mechanisms of Hepatitis B Virus X Gene Mutants on the Development of Hepatocellular Carcinoma.Frontiers in oncology · 2022Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Fueled by widespread applications of high-throughput next generation sequencing (NGS) technologies and urgent need to counter threats of pathogenic viruses, large-scale studies were conducted recently to investigate virus integration in host genomes (for example, human tumor genomes) that may cause carcinogenesis or other diseases. A limiting factor in these studies, however, is rapid virus evolution and resulting polymorphisms, which prevent reads from aligning readily to commonly used virus reference genomes, and, accordingly, make virus integration sites difficult to detect. Another confounding factor is host genomic instability as a result of virus insertions. To tackle these challenges and improve our capability to identify cryptic virus-host fusions, we present a new approach that detects Virus intEgration sites through iterative Reference SEquence customization (VERSE). To the best of our knowledge, VERSE is the first approach to improve detection through customizing reference genomes. Using 19 human tumors and cancer cell lines as test data, we demonstrated that VERSE substantially enhanced the sensitivity of virus integration site detection. VERSE is implemented in the open source package VirusFinder 2 that is available at http://bioinfo.mc.vanderbilt.edu/VirusFinder/.
Identifiers
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.