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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

https://doi.org/10.1093/bioinformatics/btu523
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Quantitative tracking of T cell clones after haematopoietic stem cell transplantation
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Naive CD4+ T Cell Frequency Varies for Different Epitopes and Predicts Repertoire Diversity and Response Magnitude
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Combination of MHC–peptide multimer-based T cell sorting with the Immunoscope permits sensitive ex vivo quantitation and follow-up of human CD8+ T cell immune responses
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Maximum entropy models for antibody diversity
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Structural basis for enabling T-cell receptor diversity within biased virus-specific CD8 + T-cell responses
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Public and private V beta T cell receptor repertoires against hen egg white lysozyme (HEL) in nontransgenic versus HEL transgenic mice.
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Application of asymmetric statistical potentials to antibody–protein docking
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Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine
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Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing
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/10.1109/iccv.1999.790410openalex-snapshot
Object recognition from local scale-invariant features
inferredcites →https://doi.org/10.1111/cei.12035openalex-snapshot
T cell receptor variable β gene repertoire in liver and peripheral blood lymphocytes of chronically hepatitis C virus-infected patients with and without mixed cryoglobulinaemia
inferredcites →https://doi.org/10.1111/imr.12006openalex-snapshot
Diversity‐oriented approaches for interrogating T‐cell receptor repertoire, ligand recognition, and function
inferredcites →https://doi.org/10.1126/science.1124228openalex-snapshot
Naïve and Memory CD4 + T Cell Survival Controlled by Clonal Abundance
inferredcites →https://doi.org/10.1126/science.1170020openalex-snapshot
High-Throughput Sequencing of the Zebrafish Antibody Repertoire
inferredcites →https://doi.org/10.1126/scitranslmed.3003656openalex-snapshot
High-Throughput Sequencing Detects Minimal Residual Disease in Acute T Lymphoblastic Leukemia
inferredcites →https://doi.org/10.1146/annurev.immunol.23.021704.115658openalex-snapshot
HOW TCRS BIND MHCS, PEPTIDES, AND CORECEPTORS
inferredcites →https://doi.org/10.1162/153244302760200687openalex-snapshot
10.1162/153244302760200687
inferredcites →https://doi.org/10.1172/jci28277openalex-snapshot
A public T cell clonotype within a heterogeneous autoreactive repertoire is dominant in driving EAE
inferredcites →https://doi.org/10.1172/jci44752openalex-snapshot
Paired analysis of TCRα and TCRβ chains at the single-cell level in mice
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/10.1186/1471-2172-14-35openalex-snapshot
Quantification of total T-cell receptor diversity by flow cytometry and spectratyping
inferredcites →https://doi.org/10.1371/journal.pone.0086986openalex-snapshot
Revealing Individual Signatures of Human T Cell CDR3 Sequence Repertoires with Kidera Factors
inferredcites →https://doi.org/10.1371/journal.ppat.1002889openalex-snapshot
Deep Sequencing of Antiviral T-Cell Responses to HCMV and EBV in Humans Reveals a Stable Repertoire That Is Maintained for Many Years
inferredcites →https://doi.org/10.3324/haematol.2012.069708openalex-snapshot
Next-generation-sequencing-spectratyping reveals public T-cell receptor repertoires in pediatric very severe aplastic anemia and identifies a chain CDR3 sequence associated with hepatitis-induced pathogenesis
inferredcites →https://doi.org/10.4049/jimmunol.1000812openalex-snapshot
Broad Cross-Reactive TCR Repertoires Recognizing Dissimilar Epstein-Barr and Influenza A Virus Epitopes
inferredcites →https://doi.org/10.4049/jimmunol.1003898openalex-snapshot
A Mechanism for TCR Sharing between T Cell Subsets and Individuals Revealed by Pyrosequencing
inferredcites →https://doi.org/10.5962/bhl.title.8281openalex-snapshot
The clonal selection theory of acquired immunity

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Population Based Selection Shapes the T Cell Receptor Repertoire During Thymic Development
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Sequence-Based TCR-Peptide Representations Using Cross-Epitope Contrastive Fine-Tuning of Protein Language Models
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Sampling from T Cell Receptor Repertoires
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Checkpoint blockade immunotherapy enhances the frequency and effector function of murine tumor-infiltrating T cells but does not alter TCRβ diversity
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Low-frequency CD8+ T cells induced by SIGN-R1+ macrophage-targeted vaccine confer SARS-CoV-2 clearance in mice
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Predicting evolution
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SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8+ T cells
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Fluctuating fitness shapes the clone-size distribution of immune repertoires
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A high density of tertiary lymphoid structure B cells in lung tumors is associated with increased CD4+T cell receptor repertoire clonality
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Predictability of antigen binding based on short motifs in the antibody CDRH3
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DiffPaSS—high-performance differentiable pairing of protein sequences using soft scores
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Feature selection using a one dimensional naïve Bayes’ classifier increases the accuracy of support vector machine classification of CDR3 repertoires
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On the viability of unsupervised T-cell receptor sequence clustering for epitope preference
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Distinctive T-cell receptor repertoire in paediatric inflammatory multisystem syndrome temporally associated with coronavirus disease 2019/multisystem inflammatory syndrome in children patients: possible thymus involvement
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Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification
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Biophysicochemical Motifs in T-cell Receptor Sequences Distinguish Repertoires from Tumor-Infiltrating Lymphocyte and Adjacent Healthy Tissue
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Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning
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Clustering based approach for population level identification of condition-associated T-cell receptor β-chain CDR3 sequences
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Phylogenetic relationships and divergent evolution in Pueraria sensu stricto (Fabaceae) based on plastid genomes and nrITS sequences
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TCRβ repertoire of CD4+ and CD8+ T cells is distinct in richness, distribution, and CDR3 amino acid composition
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Population variability in the generation and selection of T-cell repertoires
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Evaluating the utility of amino acid similarity-aware kmers to represent TCR repertoires for classification
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CD154 Costimulation Shifts the Local T-Cell Receptor Repertoire Not Only During Thymic Selection but Also During Peripheral T-Dependent Humoral Immune Responses
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RepSeq Data Representativeness and Robustness Assessment by Shannon Entropy
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sumrep: A Summary Statistic Framework for Immune Receptor Repertoire Comparison and Model Validation
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Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors
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A Conserved TCRβ Signature Dominates a Highly Polyclonal T-Cell Expansion During the Acute Phase of a Murine Malaria Infection
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Machine Learning Analysis of Naïve B-Cell Receptor Repertoires Stratifies Celiac Disease Patients and Controls
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Comparative Study of Repertoire Classification Methods Reveals Data Efficiency of k-mer Feature Extraction
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A hierarchy of selection pressures determines the organization of the T cell receptor repertoire
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Antigen-specificity measurements are the key to understanding T cell responses
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Diversity Generator Mechanisms Are Essential Components of Biological Systems: The Two Queen Hypothesis
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Disorder and the Neural Representation of Complex Odors
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Predicting T Cell Receptor Antigen Specificity From Structural Features Derived From Homology Models of Receptor-Peptide-Major Histocompatibility Complexes
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A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding
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Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires
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Deep sequencing of B cell receptor repertoire
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Additional file 1 of Clustering based approach for population level identification of condition-associated T-cell receptor β-chain CDR3 sequences
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Role and prognostic importance of regulatory T cells in lung cancer patients, according to the presence of tertiary lymphoid structures
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Optimal immune systems : a ressource allocation and information processing view of immune defense
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Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves
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Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity
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The clonal structure and dynamics of the human T cell response to an organic chemical hapten
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Early life imprints the hierarchy of T cell clone sizes
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Receptor repertoires of murine follicular T helper cells reveal a high clonal overlap in separate lymph nodes in autoimmunity
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Quantifying changes in the T cell receptor repertoire during thymic development
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Distinct T Cell Receptor (TCR) gene segment usage and MHC-restriction between foetal and adult thymus
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