VDJdb: a curated database of T-cell receptors with known antigen specificity
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VDJdb: a curated database of T-cell receptors with known antigen specificity
metasource: Fairsharing.org
version: FAIRsharing.org: VDJdb; VDJdb: a curated database of T-cell receptors with known antigen specificity; DOI: https://doi.org/10.25504/FAIRsharing.nwz68; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
VDJdb
metasource: Fairsharing.org
version: FAIRsharing.org: VDJdb; VDJdb: a curated database of T-cell receptors with known antigen specificity; DOI: https://doi.org/10.25504/FAIRsharing.nwz68; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:03.092832
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:03.092832
Names
More detailed information about this field from each metasource.
VDJdb: a curated database of T-cell receptors with known antigen specificity
metasource: Fairsharing.orgversion: FAIRsharing.org: VDJdb; VDJdb: a curated database of T-cell receptors with known antigen specificity; DOI: https://doi.org/10.25504/FAIRsharing.nwz68; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
VDJdb
metasource: Fairsharing.orgversion: FAIRsharing.org: VDJdb; VDJdb: a curated database of T-cell receptors with known antigen specificity; DOI: https://doi.org/10.25504/FAIRsharing.nwz68; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:03.092832
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:03.092832
Names
More detailed information about this field from each metasource.
VDJdb: a curated database of T-cell receptors with known antigen specificity
metasource: Fairsharing.orgversion: FAIRsharing.org: VDJdb; VDJdb: a curated database of T-cell receptors with known antigen specificity; DOI: https://doi.org/10.25504/FAIRsharing.nwz68; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
VDJdb
metasource: Fairsharing.orgversion: FAIRsharing.org: VDJdb; VDJdb: a curated database of T-cell receptors with known antigen specificity; DOI: https://doi.org/10.25504/FAIRsharing.nwz68; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:03.092832
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:03.092832
The primary goal of VDJdb is to facilitate access to existing information on T-cell receptor antigen specificities, i.e. the ability to recognize certain epitopes in certain MHC contexts. Our mission is to both aggregate the scarce TCR specificity information available so far and to create a curated repository to store such data. In addition to routine database updates providing the most up-to-date information, we make our best to ensure data consistency and fight irregularities in TCR specificity reporting with a complex database validation scheme.
Description
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The primary goal of VDJdb is to facilitate access to existing information on T-cell receptor antigen specificities, i.e. the ability to recognize certain epitopes in certain MHC contexts. Our mission is to both aggregate the scarce TCR specificity information available so far and to create a curated repository to store such data. In addition to routine database updates providing the most up-to-date information, we make our best to ensure data consistency and fight irregularities in TCR specificity reporting with a complex database validation scheme.
metasource: Fairsharing.orgversion: FAIRsharing.org: VDJdb; VDJdb: a curated database of T-cell receptors with known antigen specificity; DOI: https://doi.org/10.25504/FAIRsharing.nwz68; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The primary goal of VDJdb is to facilitate access to existing information on T-cell receptor antigen specificities, i.e. the ability to recognize certain epitopes in certain MHC contexts. Our mission is to both aggregate the scarce TCR specificity information available so far and to create a curated repository to store such data. In addition to routine database updates providing the most up-to-date information, we make our best to ensure data consistency and fight irregularities in TCR specificity reporting with a complex database validation scheme: We take into account all available information on experimental setup used to identify antigen-specific TCR sequences and assign a single confidence score to highligh most reliable records at the database generation stage. Each database record is also automatically checked against a database of V/J segment germline sequences to ensure standardized and consistent reporting of V-J junctions and CDR3 sequences that define T-cell clones.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
VDJdb is a database extension, new analysis infrastructure and a T-cell receptor motif compendium.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:03.092832
Webpage:
https://vdjdb.cdr3.netWebpage
More detailed information about this field from each metasource.
https://vdjdb.cdr3.net
metasource: Fairsharing.orgversion: FAIRsharing.org: VDJdb; VDJdb: a curated database of T-cell receptors with known antigen specificity; DOI: https://doi.org/10.25504/FAIRsharing.nwz68; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:03.092832
https://vdjdb.cdr3.net/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)Licence name
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Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: VDJdb; VDJdb: a curated database of T-cell receptors with known antigen specificity; DOI: https://doi.org/10.25504/FAIRsharing.nwz68; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Licence URL
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https://creativecommons.org/licenses/by-nc/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: VDJdb; VDJdb: a curated database of T-cell receptors with known antigen specificity; DOI: https://doi.org/10.25504/FAIRsharing.nwz68; Last edited: Jan. 8, 2019, 1:25 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium
PMID: 31588507
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:03.092832
http://dx.doi.org/10.1093/nar/gkx760
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium
PMID: 31588507
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:03.092832
http://dx.doi.org/10.1093/nar/gkx760
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium
PubMed citations: 86.
86 articles citing: VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium
Machine Learning Approaches to TCR Repertoire Analysis. PMID:35911778
Resolving SARS-CoV-2 CD4+ T cell specificity via reverse epitope discovery. PMID:35841887
DECODE: a computational pipeline to discover T cell receptor binding rules. PMID:35758821
Impaired humoral immunity is associated with prolonged COVID-19 despite robust CD8 T cell responses. PMID:35679859
CAD v1.0: Cancer Antigens Database Platform for Cancer Antigen Algorithm Development and Information Exploration. PMID:35646870
Divergent Characteristics of T-Cell Receptor Repertoire Between Essential Hypertension and Aldosterone-Producing Adenoma. PMID:35619691
Serial Analysis of the T-Cell Receptor β-Chain Repertoire in People Living With HIV Reveals Incomplete Recovery After Long-Term Antiretroviral Therapy. PMID:35585986
Distinct phenotypic states and spatial distribution of CD8+ T cell clonotypes in human brain metastases. PMID:35584630
Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA. PMID:35484264
Rapid synchronous type 1 IFN and virus-specific T cell responses characterize first wave non-severe SARS-CoV-2 infections. PMID:35474751
Single-cell RNA sequencing coupled to TCR profiling of large granular lymphocyte leukemia T cells. PMID:35411048
The CSF in neurosarcoidosis contains consistent clonal expansion of CD8 T cells, but not CD4 T cells. PMID:35405431
Pinpointing the tumor-specific T cells via TCR clusters. PMID:35377314
A blood atlas of COVID-19 defines hallmarks of disease severity and specificity. PMID:35216673
Multiple early factors anticipate post-acute COVID-19 sequelae. PMID:35216672
Identification of novel STAT5B mutations and characterization of TCRβ signatures in CD4+ T-cell large granular lymphocyte leukemia. PMID:35210405
Haematopoietic Stem Cell Transplantation Results in Extensive Remodelling of the Clonal T Cell Repertoire in Multiple Sclerosis. PMID:35197974
Activation and expansion of T-follicular helper cells in chronic lymphocytic leukemia nurselike cell co-cultures. PMID:35149845
HLA-dependent variation in SARS-CoV-2 CD8 + T cell cross-reactivity with human coronaviruses. PMID:35143694
Corrigendum: Predicting T Cell Receptor Antigen Specificity From Structural Features Derived From Homology Models of Receptor-Peptide-Major Histocompatibility Complexes. PMID:35140630
Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers. PMID:35113651
Analysis of T-Cell Receptor Repertoire in Transplantation: Fingerprint of T Cell-mediated Alloresponse. PMID:35095851
Changes in T-cell subsets and clonal repertoire during chemoimmunotherapy with pembrolizumab and paclitaxel or capecitabine for metastatic triple-negative breast cancer. PMID:35086949
ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data. PMID:34991455
Polymorphonuclear Cells Show Features of Dysfunctional Activation During Fatal Sepsis. PMID:34966382
T-Cell Receptor Repertoire Analysis with Computational Tools-An Immunologist's Perspective. PMID:34944090
A Framework to Identify Antigen-Expanded T Cell Receptor Clusters Within Complex Repertoires. PMID:34917073
Using the T Cell Receptor as a Biomarker in Type 1 Diabetes. PMID:34868047
Follicular T cells are clonally and transcriptionally distinct in B cell-driven mouse autoimmune disease. PMID:34795279
Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy. PMID:34758319
Insights From Single Cell RNA Sequencing Into the Immunology of Type 1 Diabetes- Cell Phenotypes and Antigen Specificity. PMID:34659258
Features of repertoire diversity and gene expression in human cytotoxic T cells following allogeneic hematopoietic cell transplantation. PMID:34635773
T Cell Epitope Prediction and Its Application to Immunotherapy. PMID:34603286
Immune checkpoint blockade sensitivity and progression-free survival associates with baseline CD8+ T cell clone size and cytotoxicity. PMID:34597125
Analysis of T cell receptor clonotypes in tumor microenvironment identifies shared cancer-type-specific signatures. PMID:34580764
Predicting T Cell Receptor Antigen Specificity From Structural Features Derived From Homology Models of Receptor-Peptide-Major Histocompatibility Complexes. PMID:34566692
Characteristics of T-cell receptor repertoire of stem cell-like memory CD4+ T cells. PMID:34527440
NetTCR-2.0 enables accurate prediction of TCR-peptide binding by using paired TCRα and β sequence data. PMID:34508155
Landscape of T-cell repertoires with public COVID-19-associated T-cell receptors in pre-pandemic risk cohorts. PMID:34484739
TCR repertoire characteristics predict clinical response to adoptive CTL therapy against nasopharyngeal carcinoma. PMID:34377592
Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers. PMID:34290408
High-throughput and single-cell T cell receptor sequencing technologies. PMID:34282327
TITAN: T-cell receptor specificity prediction with bimodal attention networks. PMID:34252922
CD8+ T cells specific for conserved coronavirus epitopes correlate with milder disease in COVID-19 patients. PMID:34210785
DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity. PMID:34009266
A framework for highly multiplexed dextramer mapping and prediction of T cell receptor sequences to antigen specificity. PMID:33990328
Profiling of T Cell Repertoire in SARS-CoV-2-Infected COVID-19 Patients Between Mild Disease and Pneumonia. PMID:33950324
Predicting TCR-Epitope Binding Specificity Using Deep Metric Learning and Multimodal Learning. PMID:33920780
Response to Hypomethylating Agents in Myelodysplastic Syndrome Is Associated With Emergence of Novel TCR Clonotypes. PMID:33912187
Clonally Focused Public and Private T Cells in Resected Brain Tissue From Surgeries to Treat Children With Intractable Seizures. PMID:33889159
T Cell Receptor Repertoires Acquired via Routine Pap Testing May Help Refine Cervical Cancer and Precancer Risk Estimates. PMID:33868241
Deep generative selection models of T and B cell receptor repertoires with soNNia. PMID:33795515
The Future of Blood Testing Is the Immunome. PMID:33790897
TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors. PMID:33777034
In vitro and ex vivo functional characterization of human HLA-DRB1∗04 restricted T cell receptors. PMID:33768201
Persistent T Cell Repertoire Perturbation and T Cell Activation in HIV After Long Term Treatment. PMID:33732256
Progressive immune dysfunction with advancing disease stage in renal cell carcinoma. PMID:33711273
VJ Segment Usage of TCR-Beta Repertoire in Monozygotic Cystic Fibrosis Twins. PMID:33708199
Surface NKG2C Identifies Differentiated αβT-Cell Clones Expanded in Peripheral Blood. PMID:33664730
CD8+ T-Cell Repertoire in Human Leukocyte Antigen Class I-Mismatched Alloreactive Immune Response. PMID:33552048
Tumour heterogeneity and intercellular networks of nasopharyngeal carcinoma at single cell resolution. PMID:33531485
Droplet-based mRNA sequencing of fixed and permeabilized cells by CLInt-seq allows for antigen-specific TCR cloning. PMID:33431692
Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection. PMID:33399535
DeepImmuno: Deep learning-empowered prediction and generation of immunogenic peptides for T cell immunity. PMID:33398286
Comprehensive analysis of TCR repertoire in COVID-19 using single cell sequencing. PMID:33383142
Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification. PMID:33346826
T-cell receptor repertoire of cytomegalovirus-specific cytotoxic T-cells after allogeneic stem cell transplantation. PMID:33335252
Adult-Onset Anti-Citrullinated Peptide Antibody-Negative Destructive Rheumatoid Arthritis Is Characterized by a Disease-Specific CD8+ T Lymphocyte Signature. PMID:33329548
SARS-CoV-2 Epitopes Are Recognized by a Public and Diverse Repertoire of Human T Cell Receptors. PMID:33326767
Population variability in the generation and selection of T-cell repertoires. PMID:33296360
T-cell tracking, safety, and effect of low-dose donor memory T-cell infusions after αβ T cell-depleted hematopoietic stem cell transplantation. PMID:33203952
Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors. PMID:33193332
Epitope similarity cannot explain the pre-formed T cell immunity towards structural SARS-CoV-2 proteins. PMID:33149224
Public and private human T-cell clones respond differentially to HCMV antigen when boosted by CD3 copotentiation. PMID:33125463
TCRdb: a comprehensive database for T-cell receptor sequences with powerful search function. PMID:32990749
Ultra-efficient sequencing of T Cell receptor repertoires reveals shared responses in muscle from patients with Myositis. PMID:32891935
Methods for sequence and structural analysis of B and T cell receptor repertoires. PMID:32802272
Predicting antigen specificity of single T cells based on TCR CDR3 regions. PMID:32779888
CD4+ T Cells Recognize Conserved Influenza A Epitopes through Shared Patterns of V-Gene Usage and Complementary Biochemical Features. PMID:32668259
Uncovering the Tumor Antigen Landscape: What to Know about the Discovery Process. PMID:32585818
Endocrine Autoimmune Disease as a Fragility of Immune Surveillance against Hypersecreting Mutants. PMID:32433950
Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening. PMID:32341563
Postvaccination graft dysfunction/aplastic anemia relapse with massive clonal expansion of autologous CD8+ lymphocytes. PMID:32267929
Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex. PMID:32163410
The 27th annual Nucleic Acids Research database issue and molecular biology database collection. PMID:31906604
An overview of immunoinformatics approaches and databases linking T cell receptor repertoires to their antigen specificity. PMID:31741011 - http://dx.doi.org/10.1093/nar/gkx760
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protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein sequence motifs and active sites
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
immunoproteins and antigens
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:03.092832
sequence sites, features and motifs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:03.092832
data submission, annotation and curation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:03.092832
bioinformatics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:03.092832
Tags
More detailed information about this field from each metasource.
protein sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein sequence motifs and active sites
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
immunoproteins and antigens
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:03.092832
sequence sites, features and motifs
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:03.092832
data submission, annotation and curation
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:03.092832
bioinformatics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:29:03.092832
protein sequence protein sequence motifs and active sites immunoproteins and antigens sequence sites, features and motifs data submission, annotation and curation bioinformatics
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