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Clustering based approach for population level identification of condition-associated T-cell receptor β-chain CDR3 sequences

https://doi.org/10.1101/490102
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Stereotyped B Cell Receptors in B Cell Leukemias and Lymphomas
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System-wide Analysis of the T Cell Response
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Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
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Biased T Cell Receptor Usage Directed against Human Leukocyte Antigen DQ8-Restricted Gliadin Peptides Is Associated with Celiac Disease
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T cell receptor diversity in the human thymus
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Determinants of public T cell responses
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TCR sequencing of single cells reactive to DQ2.5-glia-α2 and DQ2.5-glia-ω2 reveals clonal expansion and epitope-specific V-gene usage
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Quantifiable predictive features define epitope-specific T cell receptor repertoires
inferredcites →https://doi.org/10.1038/nature22976openalex-snapshot
Identifying specificity groups in the T cell receptor repertoire
inferredcites →https://doi.org/10.1038/ng.3822openalex-snapshot
Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire
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The molecular basis for public T-cell responses?
inferredcites →https://doi.org/10.1038/nsmb.2817openalex-snapshot
T-cell receptor recognition of HLA-DQ2–gliadin complexes associated with celiac disease
inferredcites →https://doi.org/10.1038/s41598-017-18137-9openalex-snapshot
Deep sequencing of blood and gut T-cell receptor β-chains reveals gluten-induced immune signatures in celiac disease
inferredcites →https://doi.org/10.1073/pnas.0408677102openalex-snapshot
Solving the protein sequence metric problem
inferredcites →https://doi.org/10.1073/pnas.1311861110openalex-snapshot
Dietary gluten triggers concomitant activation of CD4 + and CD8 + αβ T cells and γδ T cells in celiac disease
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Diversity and clonal selection in the human T-cell repertoire
inferredcites →https://doi.org/10.1093/bioinformatics/btm563openalex-snapshot
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R
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Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence
inferredcites →https://doi.org/10.1093/bioinformatics/btx286openalex-snapshot
McPAS-TCR: a manually curated catalogue of pathology-associated T cell receptor sequences
inferredcites →https://doi.org/10.1093/intimm/dxt037openalex-snapshot
Biased usage and preferred pairing of α- and β-chains of TCRs specific for an immunodominant gluten epitope in coeliac disease
inferredcites →https://doi.org/10.1093/nar/gku1056openalex-snapshot
IMGT®, the international ImMunoGeneTics information system® 25 years on
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VDJdb: a curated database of T-cell receptor sequences with known antigen specificity
inferredcites →https://doi.org/10.1101/gr.170753.113openalex-snapshot
T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity
inferredcites →https://doi.org/10.1111/j.1365-2567.2011.03527.xopenalex-snapshot
Rep‐Seq: uncovering the immunological repertoire through next‐generation sequencing
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Dynamics of the Cytotoxic T Cell Response to a Model of Acute Viral Infection
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Public T cell receptors confer high-avidity CD4 responses to HIV controllers
inferredcites →https://doi.org/10.1172/jci98819openalex-snapshot
Disease-driving CD4+ T cell clonotypes persist for decades in celiac disease
inferredcites →https://doi.org/10.1177/154405910408300516openalex-snapshot
Indian Hedgehog: A Mechanotransduction Mediator in Condylar Cartilage
inferredcites →https://doi.org/10.1182/blood-2009-04-217604openalex-snapshot
Comprehensive assessment of T-cell receptor β-chain diversity in αβ T cells
inferredcites →https://doi.org/10.1182/blood-2011-11-393694openalex-snapshot
Stereotyped B-cell receptors in one-third of chronic lymphocytic leukemia: a molecular classification with implications for targeted therapies
inferredcites →https://doi.org/10.1371/journal.pbio.3000314openalex-snapshot
Detecting T cell receptors involved in immune responses from single repertoire snapshots
inferredcites →https://doi.org/10.4049/jimmunol.1101526openalex-snapshot
Posttranslational Modification of Gluten Shapes TCR Usage in Celiac Disease
inferredcites →https://doi.org/10.4049/jimmunol.1601693openalex-snapshot
T Cells in Celiac Disease
inferredcites →https://doi.org/10.4049/jimmunol.1700594openalex-snapshot
Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires
inferredcites →https://doi.org/10.7554/elife.33050openalex-snapshot
Method for identification of condition-associated public antigen receptor sequences
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