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References from Mapping the TCR landscape: computational tools empowering translational immunology and therapy design. Local targets link to admitted publications; unresolved targets remain external evidence.
Evaluation of the TCR Repertoire as a Predictive and Prognostic Biomarker in Cancer: Diversity or Clonality?
10.3390/cancers14071771 · 2022 · External reference
10.1038/s41577-020-0306
10.1038/s41577-020-0306 · External reference
10.1111/imr.12772
10.1111/imr.12772 · External reference
10.1074/jbc.rev119.009411
10.1074/jbc.rev119.009411 · External reference
Molecular T-Cell Repertoire Analysis as Source of Prognostic and Predictive Biomarkers for Checkpoint Blockade Immunotherapy
10.3390/ijms21072378 · 2020 · External reference
T-cell antigen receptor genes and T-cell recognition
10.1038/334395a0 · 1988 · External reference
10.1016/j.smim.2023.101810
10.1016/j.smim.2023.101810 · External reference
Regulation of T-cell Receptor Gene Expression by Three-Dimensional Locus Conformation and Enhancer Function
10.3390/ijms21228478 · 2020 · External reference
10.1038/ni1379
10.1038/ni1379 · External reference
10.1126/science.8211163
10.1126/science.8211163 · External reference
10.1073/pnas.95.9.5217
10.1073/pnas.95.9.5217 · External reference
10.1002/eji.200323961
10.1002/eji.200323961 · External reference
Early events in TCR signaling - the evolving role of ITAMs
10.3389/fimmu.2025.1563049 · 2025 · External reference
Adapting T Cell Receptor Ligand Discrimination Capability via LAT
10.3389/fimmu.2021.673196 · 2021 · External reference
High frequency of shared clonotypes in human B cell receptor repertoires
10.1038/s41586-019-0934-8 · 2019 · External reference
Strategies and rules for tuning TCR-derived therapy
10.1017/erm.2023.27 · 2023 · External reference
10.1016/j.coi.2015.02.005
10.1016/j.coi.2015.02.005 · External reference
Comparative Analysis of the CDR Loops of Antigen Receptors
10.3389/fimmu.2019.02454 · 2019 · External reference
Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy
10.3389/fimmu.2017.01210 · 2017 · External reference
Unveiling cross-reactivity: implications for immune response modulation in cancer
10.1093/bib/bbaf012 · 2024 · External reference
Complementarity-determining region clustering may cause CAR-T cell dysfunction
10.1038/s41467-023-40303-z · 2023 · External reference
In Situ Vaccination by Tumor Ablation: Principles and Prospects for Systemic Antitumor Immunity
10.3390/vaccines13111114 · 2025 · External reference
10.1158/2326-6066.cir-22-0961
10.1158/2326-6066.cir-22-0961 · External reference
10.1158/2159-8290.cd-17-1418
10.1158/2159-8290.cd-17-1418 · External reference
Selection of therapeutically effective T-cell receptors from the diverse tumor-bearing repertoire
10.1136/jitc-2024-011351 · 2025 · External reference
Overview of methodologies for T-cell receptor repertoire analysis
10.1186/s12896-017-0379-9 · 2017 · External reference
10.1158/1078-0432.ccr-22-2469
10.1158/1078-0432.ccr-22-2469 · External reference
10.1038/s41592-021-01201-8
10.1038/s41592-021-01201-8 · External reference
Single-cell meta-analysis of T cells reveals clonal dynamics of response to checkpoint immunotherapy
10.1016/j.xgen.2025.100842 · 2025 · External reference
10.1007/s00251-009-0383-x
10.1007/s00251-009-0383-x · External reference
Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling
10.1186/s12864-020-07358-4 · 2021 · External reference
10.1093/bib/bbz092
10.1093/bib/bbz092 · External reference
T-Cell Receptor Repertoire Sequencing and Its Applications: Focus on Infectious Diseases and Cancer
10.3390/ijms23158590 · 2022 · External reference
T-Cell Receptor Repertoire Analysis with Computational Tools—An Immunologist’s Perspective
10.3390/cells10123582 · 2021 · External reference
10.1101/2025.01.12.632367
10.1101/2025.01.12.632367 · External reference
TCRdb 2.0: an updated T-cell receptor sequence database
10.1093/nar/gkaf876 · 2026 · External reference
Biomarkers of aging: immunological events
10.1016/0531-5565(88)90042-3 · 1988 · External reference
Impact of immunological aging on T cell-mediated therapies in older adults with multiple myeloma and lymphoma
10.1136/jitc-2024-009462 · 2024 · External reference
10.1073/pnas.2023216118
10.1073/pnas.2023216118 · External reference
Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing
10.1093/bib/bbad220 · 2023 · External reference
10.1101/2025.08.05.668736
10.1101/2025.08.05.668736 · External reference
10.1038/nmeth.3364
10.1038/nmeth.3364 · External reference
Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis
10.1007/978-1-0716-2115-8_17 · 2022 · External reference
Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: Relevance in infectious diseases and vaccination studies in human populations
10.1038/s41435-021-00143-7 · 2021 · External reference
10.1111/j.1365-2567.2011.03527.x
10.1111/j.1365-2567.2011.03527.x · External reference
10.1038/s41592-021-01142-2
10.1038/s41592-021-01142-2 · External reference
10.1038/nmeth.3800
10.1038/nmeth.3800 · External reference
Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing
10.1186/1471-2164-15-409 · 2014 · External reference
Structure of the complex between human T-cell receptor, viral peptide and HLA-A2
10.1038/384134a0 · 1996 · External reference
10.1146/annurev-immunol-032414-112334
10.1146/annurev-immunol-032414-112334 · External reference
T cell receptor convergence is an indicator of antigen-specific T cell response in cancer immunotherapies
10.7554/elife.81952 · 2022 · External reference
10.1073/pnas.89.22.10915
10.1073/pnas.89.22.10915 · External reference
Quantifiable predictive features define epitope-specific T cell receptor repertoires
10.1038/nature22383 · 2017 · External reference
10.1038/s41587-020-0505-4
10.1038/s41587-020-0505-4 · External reference
10.1158/1078-0432.ccr-19-3249
10.1158/1078-0432.ccr-19-3249 · External reference
10.1093/bioinformatics/btab446
10.1093/bioinformatics/btab446 · External reference
DeepTCR is a deep learning framework for revealing sequence concepts within T-cell repertoires
10.1038/s41467-021-21879-w · 2021 · External reference
Unresolved reference
External reference
TCR clustering by contrastive learning on antigen specificity
10.1093/bib/bbae375 · 2024 · External reference
LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity
10.1371/journal.pcbi.1011300 · 2023 · External reference
TCR Repertoire as a Novel Indicator for Immune Monitoring and Prognosis Assessment of Patients With Cervical Cancer
10.3389/fimmu.2018.02729 · 2018 · External reference
TCR repertoire characteristics predict clinical response to adoptive CTL therapy against nasopharyngeal carcinoma
10.1080/2162402x.2021.1955545 · 2021 · External reference
Benchmarking unsupervised methods for inferring TCR specificity
10.1093/nargab/lqaf150 · 2025 · External reference
Molecular Rules Underpinning Enhanced Affinity Binding of Human T Cell Receptors Engineered for Immunotherapy
10.1016/j.omto.2020.07.008 · 2020 · External reference
T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity
10.1038/s42003-025-07708-6 · 2025 · External reference
TCR3d 2.0: expanding the T cell receptor structure database with new structures, tools and interactions
10.1093/nar/gkae840 · 2025 · External reference
Unresolved reference
External reference
Structural allele-specific patterns adopted by epitopes in the MHC-I cleft and reconstruction of MHC:peptide complexes to cross-reactivity assessment
10.1371/journal.pone.0010353 · 2010 · External reference
10.1021/acs.jcim.5c00298
10.1021/acs.jcim.5c00298 · External reference
Strengths and limitations of web servers for the modeling of TCRpMHC complexes
10.1016/j.csbj.2024.06.028 · 2024 · External reference
10.1093/nar/gkv535
10.1093/nar/gkv535 · External reference
10.1038/s41586-021-03819-2
10.1038/s41586-021-03819-2 · External reference
10.1038/s41586-024-07487-w
10.1038/s41586-024-07487-w · External reference
Current progress and open challenges for applying deep learning across the biosciences
10.1038/s41467-022-29268-7 · 2022 · External reference
Structural characterization and AlphaFold modeling of human T cell receptor recognition of NRAS cancer neoantigens
10.1126/sciadv.adq6150 · 2024 · External reference
10.1016/j.coi.2021.07.006
10.1016/j.coi.2021.07.006 · External reference
10.1093/nar/gkad356
10.1093/nar/gkad356 · External reference
ImmuneBuilder: Deep-Learning models for predicting the structures of immune proteins
10.1038/s42003-023-04927-7 · 2023 · External reference
10.1101/2024.05.20.594940
10.1101/2024.05.20.594940 · External reference
10.1101/2021.10.04.463034
10.1101/2021.10.04.463034 · External reference
DockQ: A Quality Measure for Protein-Protein Docking Models
10.1371/journal.pone.0161879 · 2016 · External reference
10.1093/nar/gkx971
10.1093/nar/gkx971 · External reference
Structure-based prediction of T cell receptor:peptide-MHC interactions
10.7554/elife.82813 · 2023 · External reference
High resolution mapping of protein motions in time and space with RMSX and Flipbook
10.1038/s41598-026-39869-7 · 2026 · External reference
NetTCR-struc, a structure driven approach for prediction of TCR-pMHC interactions
10.3389/fimmu.2025.1616328 · 2025 · External reference
10.1016/j.csbj.2025.09.004 · Admitted local publication
10.1109/tcbbio.2024.3504235
10.1109/tcbbio.2024.3504235 · External reference
TCRcost: a deep learning model utilizing TCR 3D structure for enhanced of TCR–peptide binding
10.3389/fgene.2024.1346784 · 2024 · External reference
Pan-Peptide Meta Learning for T-cell receptor–antigen binding recognition
10.1038/s42256-023-00619-3 · 2023 · External reference
TPepRet: a deep learning model for characterizing T-cell receptors-antigen binding patterns
10.1093/bioinformatics/btaf022 · 2024 · External reference
10.1093/bib/bbae420
10.1093/bib/bbae420 · External reference
10.1093/bioinformatics/btaf202
10.1093/bioinformatics/btaf202 · External reference
epiTCR: a highly sensitive predictor for TCR-peptide binding
10.1093/bioinformatics/btad284 · 2023 · External reference
BERTrand-peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing
10.1093/bioinformatics/btad468 · 2023 · External reference
10.1016/j.immuno.2024.100045
10.1016/j.immuno.2024.100045 · External reference
Neoantigens: promising targets for cancer therapy
10.1038/s41392-022-01270-x · 2023 · External reference
CrossDome: an interactive R package to predict cross-reactivity risk using immunopeptidomics databases
10.3389/fimmu.2023.1142573 · 2023 · External reference
T cell receptor cross-reactivity prediction improved by a comprehensive mutational scan database
10.1016/j.cels.2025.101345 · 2025 · External reference
10.3389/fimmu.2024.1377259
10.3389/fimmu.2024.1377259 · External reference
A kinetic gatekeeper: TCR-pMHC dissociation dynamics determine T cell activation efficacy
10.1002/pro.70346 · 2025 · External reference
10.1038/s41422-025-01077-9
10.1038/s41422-025-01077-9 · External reference
Mechanoimmunology of T-Cell Activation
10.1111/sji.70009 · 2025 · External reference
