ArticleBMC bioinformatics2015
VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 44 citations in OpenAlex.
- PRISM-Seq: An Ultra-sensitive Sequencing Approach For Mapping Lentiviral Integration Sites.bioRxiv : the preprint server for biology · 2026Article
- InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration.Database : the journal of biological databases and curation · 2023Article
- IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods.BMC bioinformatics · 2023Article
- Intraosseous delivery of platelet-targeted factor VIII lentiviral vector in humanized NBSGW mice.Blood advances · 2022Article
- Interrogation of clonal tracking data usingNature computational science · 2021Article
- Article
- DNA Barcoding in Nonhuman Primates Reveals Important Limitations in Retrovirus Integration Site Analysis.Molecular therapy. Methods & clinical development · 2020Article
- VSeq-Toolkit: Comprehensive Computational Analysis of Viral Vectors in Gene Therapy.Molecular therapy. Methods & clinical development · 2020Article
- Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy.Nature communications · 2020Article
- Autologous, Gene-Modified Hematopoietic Stem and Progenitor Cells Repopulate the Central Nervous System with Distinct Clonal Variants.Stem cell reports · 2019Article
- UM171 Enhances Lentiviral Gene Transfer and Recovery of Primitive Human Hematopoietic Cells.Molecular therapy. Methods & clinical development · 2018Article
- Efficacy and safety of a clinically relevant foamy vector design in human hematopoietic repopulating cells.The journal of gene medicine · 2018Article
- Replication-incompetent gammaretroviral and lentiviral vector-based insertional mutagenesis screens identify prostate cancer progression genes.Oncotarget · 2018Article
- VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites.BMC bioinformatics · 2017Article
- A distinct hematopoietic stem cell population for rapid multilineage engraftment in nonhuman primates.Science translational medicine · 2017Article
- VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy.BMC bioinformatics · 2017Article
- In Vivo Murine-Matured Human CD3Molecular therapy. Methods & clinical development · 2017Article
- Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data.BMC bioinformatics · 2017Article
- INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes.Molecular therapy. Methods & clinical development · 2017Article
- INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions.Molecular therapy. Methods & clinical development · 2017Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundAnalyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integration sites is also important for retroviral mutagenesis screens.
resultsWe developed VISA, a vector integration site analysis server, to analyze next-generation sequencing data for retroviral vector integration sites. Sequence reads that contain a provirus are mapped to the human genome, sequence reads that cannot be localized to a unique location in the genome are filtered out, and then unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads.
conclusionsVISA offers a simple web interface to upload sequence files and results are returned in a concise tabular format to allow rapid analysis of retroviral vector integration sites.
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.