ArticleBioinformatics (Oxford, England)2013
ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
45 citing papers in PubMed.
- Challenges in the detection and assembly of virus integration structures in human genomes.Frontiers in oncology · 2026Review
- Detection of viral contamination in cell lines using ViralCellDetector.Frontiers in microbiology · 2025Article
- Integration of Viral Genome to Human Genomic DNA in Nails of Patients with Chronic Hepatitis B Virus Infection.JMA journal · 2023Article
- Human papillomavirus integration transforms chromatin to drive oncogenesis.Genome biology · 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
- hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.International journal of molecular sciences · 2022Article
- FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA.NAR genomics and bioinformatics · 2022Article
- Causes and Consequences of HPV Integration in Head and Neck Squamous Cell Carcinomas: State of the Art.Cancers · 2021Review
- SurVirus: a repeat-aware virus integration caller.Nucleic acids research · 2021Article
- Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives.Frontiers in microbiology · 2021Review
- A First NGS Investigation Suggests No Association Between Viruses and Canine Cancers.Frontiers in veterinary science · 2020Article
- Integrated Pan-Cancer Map of EBV-Associated Neoplasms Reveals Functional Host-Virus Interactions.Cancer research · 2019Article
- The fusion landscape of hepatocellular carcinoma.Molecular oncology · 2019Article
- A virome-wide clonal integration analysis platform for discovering cancer viral etiology.Genome research · 2019Article
- Article
- Detecting virus integration sites based on multiple related sequencing data by VirTect.BMC medical genomics · 2019Article
- The precision prevention and therapy of HPV-related cervical cancer: new concepts and clinical implications.Cancer medicine · 2018Review
- HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data.BMC bioinformatics · 2018Article
- Hepatitis B virus pathogenesis: Fresh insights into hepatitis B virus RNA.World journal of gastroenterology · 2018Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryInsertional mutagenesis from virus infection is an important pathogenic risk for the development of cancer. Despite the advent of high-throughput sequencing, discovery of viral integration sites and expressed viral fusion events are still limited. Here, we present ViralFusionSeq (VFS), which combines soft-clipping information, read-pair analysis and targeted de novo assembly to discover and annotate viral-human fusions. VFS was used in an RNA-Seq experiment, simulated DNA-Seq experiment and re-analysis of published DNA-Seq datasets. Our experiments demonstrated that VFS is both sensitive and highly accurate. AVAILABILITY: VFS is distributed under GPL version 3 at http://hkbic.cuhk.edu.hk/software/viralfusionseq
Indexed as
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.