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VDJdb specifications

Information


Unique identifier OMICS_20796
Name VDJdb
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Dmitriy Chudakov

Publication for VDJdb

VDJdb citations

 (3)
library_books

Peptide–MHC Class I Tetramers Can Fail To Detect Relevant Functional T Cell Clonotypes and Underestimate Antigen Reactive T Cell Populations

2018
PMCID: 5857646
PMID: 29483360
DOI: 10.4049/jimmunol.1700242

[…] f patient MM909.24 were sequenced, and all TCRs used for analyses. Public TCRs were assigned using a curated database of TCR sequences with known Ag specificity (). TCR sequences are available at the VDJdb database (): https://github.com/antigenomics/vdjdb-db/issues/243. […]

library_books

Computational Strategies for Dissecting the High Dimensional Complexity of Adaptive Immune Repertoires

2018
Front Immunol
PMCID: 5826328
PMID: 29515569
DOI: 10.3389/fimmu.2018.00224

[…] machine learning but also a problem for network-based approaches, where one wishes to map antigen-specific information onto generated networks (, ). To address this issue for T-cells, Shugay et al. (VDJDB) and Tickotsky et al. (McPAS-TCR) have built dedicated and curated databases. VDJDB gathers >20,000 unique TCR sequences from different species associated with their epitope (>200) and MHC conte […]

library_books

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection

2017
Nucleic Acids Res
PMCID: 5753253
PMID: 29316735
DOI: 10.1093/nar/gkx1235

[…] ge through a transmembrane protein. Certain protein classes or families justify their own bespoke databases through medical or biological importance. T-cell receptors are served in this issue by both VDJdb (), focussing on receptor sequences of known specificity, and STCRDab () which collects and curates structural information, linking to and allowing searches against a wide variety of structural, […]

Citations

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VDJdb institution(s)
Pirogov Russian National Research Medical University, Moscow, Russia; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Central European Institute of Technology, Brno, Czech Republic; Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia; Theoretical Biology and Bioinformatics, Science Faculty, Utrecht University, Utrecht, Netherlands; Department of Immunology, St. Jude’s Children’s Research Hospital, Memphis, TN, USA; Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK; Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Viral Immunology Systems Program, Kirby Institute, School of Medical Sciences, University of New South Wales, Kensington, NSW, Australia; Center for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, Netherlands; Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK
VDJdb funding source(s)
Supported by Pirogov Russian National Research Medical University; European Union’s Horizon 2020 Research and Innovation Programme [633592]; Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 [LQ1601]; Wellcome Trust Senior Investigator Awards; Cancer Research Wales PhD Studentship.

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