ArticleBMC genomics2016
VDJviz: a versatile browser for immunogenomics data.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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.
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Who cites it
25 citing papers in PubMed, 34 citations in OpenAlex.
- Vaccine-expanded plasmablast-like B cells are associated with response to dendritic cell therapy in metastatic melanoma.Journal of experimental & clinical cancer research : CR · 2026Article
- Innovative Single-Cell Sequencing Techniques for B cell Analysis and Their Implications for Rational HIV-1 Vaccine Design.Current HIV research · 2026Review
- Circulating memory B-cell receptor repertoire analysis identifies novel candidate antibodies against metastatic melanoma in immunotherapy-responsive patients.Frontiers in immunology · 2025Article
- Nanopore Sequencing for T-Cell Receptor Rearrangement Analysis in Cutaneous T-Cell Lymphoma.Cancers · 2024Article
- TCRosetta: An Integrated Analysis and Annotation Platform for T-cell Receptor Sequences.Genomics, proteomics & bioinformatics · 2024Article
- TCR_Explore: A novel webtool for T cell receptor repertoire analysis.Computational and structural biotechnology journal · 2023Article
- B-cell receptor repertoire sequencing: Deeper digging into the mechanisms and clinical aspects of immune-mediated diseases.iScience · 2022Review
- AIRRscape: An interactive tool for exploring B-cell receptor repertoires and antibody responses.PLoS computational biology · 2022Article
- Article
- Haematopoietic Stem Cell Transplantation Results in Extensive Remodelling of the Clonal T Cell Repertoire in Multiple Sclerosis.Frontiers in immunology · 2022Article
- An overview of immunoinformatics approaches and databases linking T cell receptor repertoires to their antigen specificity.Immunogenetics · 2020Review
- VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium.Nucleic acids research · 2020Article
- VisTCR: An Interactive Software for T Cell Repertoire Sequencing Data Analysis.Frontiers in genetics · 2020Article
- Best practices for bioinformatic characterization of neoantigens for clinical utility.Genome medicine · 2019Review
- A Framework for Annotation of Antigen Specificities in High-Throughput T-Cell Repertoire Sequencing Studies.Frontiers in immunology · 2019Article
- Systems vaccinology and big data in the vaccine development chain.Immunology · 2019Review
- Exploring the pre-immune landscape of antigen-specific T cells.Genome medicine · 2018Article
- Plasmablast antibody repertoires in elderly influenza vaccine responders exhibit restricted diversity but increased breadth of binding across influenza strains.Clinical immunology (Orlando, Fla.) · 2018Article
- BRepertoire: a user-friendly web server for analysing antibody repertoire data.Nucleic acids research · 2018Article
- Network Representation of T-Cell Repertoire- A Novel Tool to Analyze Immune Response to Cancer Formation.Frontiers in immunology · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe repertoire of T- and B-cell receptor sequences encodes the antigen specificity of adaptive immunity system, determines its present state and guides its ability to mount effective response against encountered antigens in future. High throughput sequencing of immune repertoires (Rep-Seq) is a promising technique that allows to profile millions of antigen receptors of an individual in a single experiment. While a substantial number of tools for mapping and assembling Rep-Seq data were published recently, the field still lacks an intuitive and flexible tool that can be used by researchers with little or no computational background for in-depth analysis of immune repertoire profiles.
resultsHere we report VDJviz, a web tool that can be used to browse, analyze and perform quality control of Rep-Seq results generated by various pre-processing software. On a set of real data examples we show that VDJviz can be used to explore key repertoire characteristics such as spectratype, repertoire clonality, V-(D)-J recombination patterns and to identify shared clonotypes. We also demonstrate the utility of VDJviz in detection of critical Rep-Seq biases such as artificial repertoire diversity and cross-sample contamination.
conclusionsVDJviz is a versatile and lightweight tool that can be easily employed by biologists, immunologists and immunogeneticists for routine analysis and quality control of Rep-Seq data. The software is freely available for non-commercial purposes, and can be downloaded from: https://github.com/antigenomics/vdjviz .
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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.