ArticleBioinformatics (Oxford, England)2011
Identifying viral integration sites using SeqMap 2.0.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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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.
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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
20 citing papers in PubMed.
- IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods.BMC bioinformatics · 2023Article
- 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
- Interrogation of clonal tracking data usingNature computational science · 2021Article
- A Signature of Five Long Non-Coding RNAs for Predicting the Prognosis of Alzheimer's Disease Based on Competing Endogenous RNA Networks.Frontiers in aging neuroscience · 2020Article
- A virome-wide clonal integration analysis platform for discovering cancer viral etiology.Genome research · 2019Article
- VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites.BMC bioinformatics · 2017Article
- INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions.Molecular therapy. Methods & clinical development · 2017Article
- INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes.Molecular therapy. Methods & clinical development · 2017Article
- Differences in vector-genome processing and illegitimate integration of non-integrating lentiviral vectors.Gene therapy · 2017Article
- Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology.BMC genomics · 2016Article
- VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.BMC bioinformatics · 2015Article
- Unraveling the web of viroinformatics: computational tools and databases in virus research.Journal of virology · 2015Review
- Development and Evaluation of Quality Metrics for Bioinformatics Analysis of Viral Insertion Site Data Generated Using High Throughput Sequencing.Biomedicines · 2014Article
- VISPA: a computational pipeline for the identification and analysis of genomic vector integration sites.Genome medicine · 2014Article
- Transgenic sheep generated by lentiviral vectors: safety and integration analysis of surrogates and their offspring.Transgenic research · 2013Article
- ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.Bioinformatics (Oxford, England) · 2013Article
- Center for fetal monkey gene transfer for heart, lung, and blood diseases: an NHLBI resource for the gene therapy community.Human gene therapy · 2012Review
- Bioinformatic clonality analysis of next-generation sequencing-derived viral vector integration sites.Human gene therapy methods · 2012Article
- Dr.VIS: a database of human disease-related viral integration sites.Nucleic acids research · 2012Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
unlabelledRetroviral integration has been implicated in several biomedical applications, including identification of cancer-associated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites from long read high-throughput sequencing. Individual sequence reads are masked to remove non-genomic sequence, aligned to the host genome and assembled into contiguous fragments used to pinpoint the position of integration. AVAILABILITY AND IMPLEMENTATION: The method is implemented in a publicly accessible web server platform, SeqMap 2.0, containing analysis tools and both private and shared lab workspaces that facilitate collaboration among researchers. Available at http://seqmap.compbio.iupui.edu/.
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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.