High-throughput determination of the antigen specificities of T cell receptors in single cells

Cancer Regression and Autoimmunity in Patients After Clonal Repopulation with Antitumor Lymphocytes

Dudley, M. E., Wunderlich, J. R., Robbins, P. F., Yang, J. C., Hwu, P., Schwartzentruber, D. J., Topalian, S. L., Sherry, R., Restifo, N. P., Hubicki, A. M., et al. (2002) · Science · doi:10.1126/science.1076514 · Cited by 2,823

A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells

Carreno, B. M., Magrini, V., Becker-Hapak, M., Kaabinejadian, S., Hundal, J., Petti, A. A., Ly, A., Lie, W.-R., Hildebrand, W. H., Mardis, E. R., et al. (2015) · Science · doi:10.1126/science.aaa3828 · Cited by 1,285

Identifying specificity groups in the T cell receptor repertoire

Glanville, J., Huang, H., Nau, A., Hatton, O., Wagar, L. E., Rubelt, F., Ji, X., Han, A., Krams, S. M., Pettus, C., et al. (2017) · Nature · doi:10.1038/nature22976 · Cited by 1,026

Multiplexed quantification of proteins and transcripts in single cells

Peterson, V. M., Zhang, K. X., Kumar, N., Wong, J., Li, L., Wilson, D. C., Moore, R., McClanahan, T. K., Sadekova, S., & Klappenbach, J. A. (2017) · Nature Biotechnology · doi:10.1038/nbt.3973 · Cited by 832

Identification of a Titin-Derived HLA-A1–Presented Peptide as a Cross-Reactive Target for Engineered MAGE A3–Directed T Cells

Cameron, B., Gerry, A. B., Dukes, J. D., Harper, J. V., Kannan, V., Bianchi, F., Grand, F., Brewer, J. E., Gupta, M., Plesa, G., et al. (2013) · Science Translational Medicine · doi:10.1126/scitranslmed.3006034 · Cited by 703

Deconstructing the Peptide-MHC Specificity of T Cell Recognition

Birnbaum, M. E., Mendoza, J. L., Sethi, D. K., Dong, S., Glanville, J., Dobbins, J., Özkan, E., Davis, M. M., Wucherpfennig, K. W., & García, K. C. (2014) · Cell · doi:10.1016/j.cell.2014.03.047 · Cited by 567

Targeting of cancer neoantigens with donor-derived T cell receptor repertoires

Strønen, E., Toebes, M., Kelderman, S., van Buuren, M. M., Yang, W., van Rooij, N., Donia, M., Böschen, M.-L., Lund‐Johansen, F., Olweus, J., et al. (2016) · Science · doi:10.1126/science.aaf2288 · Cited by 453

Isolation of neoantigen-specific T cells from tumor and peripheral lymphocytes

Cohen, C. J., Gartner, J. J., Horovitz‐Fried, M., Shamalov, K., Trebska-McGowan, K., Bliskovsky, V. V., Parkhurst, M. R., Ankri, C., Prickett, T. D., Crystal, J. S., et al. (2015) · Journal of Clinical Investigation · doi:10.1172/jci82416 · Cited by 380

Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes

Bentzen, A. K., Marquard, A. M., Lyngaa, R., Saini, S. K., Ramskov, S., Donia, M., Such, L., Furness, A. J. S., McGranahan, N., Rosenthal, R., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3662 · Cited by 339

Generation of peptide–MHC class I complexes through UV-mediated ligand exchange

Rodenko, B., Toebes, M., Hadrup, S. R., van Esch, W. J. E., Molenaar, A. M., Schumacher, T. N., & Ovaa, H. (2006) · Nature Protocols · doi:10.1038/nprot.2006.121 · Cited by 320

Identification of Antigenic Targets

Gerber, H., Sibener, L. V., Lee, L. J., & Gee, M. H. (2020) · Trends in cancer · doi:10.1016/j.trecan.2020.01.002 · Cited by 12

Immortalization and functional screening of natively paired human T cell receptor repertoires

Fahad, A. S., Chung, C.-Y., Acevedo, S. N. L., Boyle, N., Madan, B., Gutiérrez-González, M., Matus‐Nicodemos, R., Laflin, A. D., Ladi, R., Zhou, J. L., et al. (2021) · Protein Engineering Design and Selection · doi:10.1093/protein/gzab034 · Cited by 14

Discordance Between the Predicted Versus the Actually Recognized CD8+ T Cell Epitopes of HCMV pp65 Antigen and Aleatory Epitope Dominance

Lehmann, A. A., Zhang, T., Reche, P. A., & Lehmann, P. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2020.618428 · Cited by 12

Thermal‐exchange HLA‐E multimers reveal specificity in HLA‐E and NKG2A / CD94 complex interactions

Ruibal, P., Derksen, I., van Wolfswinkel, M., Voogd, L., Franken, K. L. M. C., Hebieshy, A. F. E., van Hall, T., Schoufour, T. A. W., Wijdeven, R. H. M., Ottenhoff, T. H. M., et al. (2022) · Immunology · doi:10.1111/imm.13591 · Cited by 11

Insights into anti-tumor immunity via the polyomavirus shared across human Merkel cell carcinomas

Jani, S., Church, C. D., & Nghiem, P. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1172913 · Cited by 11

Interfacing Biomaterials with Synthetic T Cell Immunity

Su, F., Mac, Q. D., Sivakumar, A., & Kwong, G. A. (2021) · Advanced Healthcare Materials · doi:10.1002/adhm.202100157 · Cited by 10

Applications of high-resolution clone tracking technologies in cancer

Morgan, D., Jost, T. A., Santiago, C. D., & Brock, A. (2021) · Current Opinion in Biomedical Engineering · doi:10.1016/j.cobme.2021.100317 · Cited by 11

Decoding the CAF–TAM axis: multi-omics dissection and therapeutic targeting of stromal–immune crosstalk in the tumor microenvironment

Fu, Y., Li, M., Wu, S., Wang, J., & Wang, S. (2026) · Cell Death and Disease · doi:10.1038/s41419-026-08685-2 · Cited by 11

How single-cell techniques help us look into lung cancer heterogeneity and immunotherapy

Liao, P., Huang, Q., Zhang, J., Su, Y., Xiao, R., Luo, S., Wu, Z., Zhu, L., Li, J., & Hu, Q. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1238454 · Cited by 10

TRAIT: A Comprehensive Database for T-cell Receptor–antigen Interactions

Wei, M., Wu, J., Bai, S., Zhou, Y., Chen, Y., Zhang, X., Zhao, W., Chi, Y., Pan, G., Zhu, F., et al. (2025) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzaf033 · Cited by 13

Advances in preclinical TCR characterization: leveraging cell avidity to identify functional TCRs

Carr, A., Mateyka, L. M., Scheu, S. J. C., Bici, A., Paijmans, J., Reijmers, R. M., Dieminger, N., Dildebekova, S., Hamed, N., Wagner, K., et al. (2024) · Biological Chemistry · doi:10.1515/hsz-2023-0341 · Cited by 10

TCR sequencing in cancer immunology and immunotherapy: what, when, where, why, and how

Nose, Y., Figueiredo, I., Tuballes, K., Valle, D. M. D., Gonsalves, T. R., Guo, R., Ioannou, G., Cabal, R., Gonzalez‐Kozlova, E., & Gnjatic, S. (2026) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2025-013499 · Cited by 9

Altered MUC1 epitope-specific CTLs: A potential target for immunotherapy of pancreatic cancer

Hong, J., Guo, G., Wu, S., Lin, S., Zhou, Z., Chen, S., Ye, C., Li, J., Lin, W., & Ye, Y. (2022) · Journal of Leukocyte Biology · doi:10.1002/jlb.5ma0922-749r · Cited by 9

Needle in a Haystack: The Naïve Repertoire as a Source of T Cell Receptors for Adoptive Therapy with Engineered T Cells

D’Ippolito, E., Wagner, K. I., & Busch, D. H. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21218324 · Cited by 10

High-throughput discovery of cancer-targeting TCRs

Bunse, L., Green, E. W., & Platten, M. (2019) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2019.10.009 · Cited by 9

pan-MHC and cross-Species Prediction of T Cell Receptor-Antigen BindingPreprint

Han, Y., Yang, Y., Tian, Y., Fattah, F. J., von Itzstein, M. S., Hu, Y., Zhang, M., Kang, X., Yang, D. M., Liu, J., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.01.569599 · Cited by 10

TDP-43 pathology induces CD8 + T cell activation through cryptic epitope recognitionPreprint

Chizari, S., Zanovello, M., Kong, S. L., Saigal, V. J., Brown, A., Turchetti, V., Chen, B., Devine, C. C., Zampedri, L., Skorupinska, I., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.22.660773 · Cited by 12

TPepRet: a deep learning model for characterizing T-cell receptors–antigen binding patterns

Wang, M., Fan, W., Wu, T., & Li, M. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btaf022 · Cited by 8

THLANet: A deep learning framework for predicting TCR-pHLA binding in immunotherapy applications

Xu, L., Yang, Q., Dong, W., Li, X., Wang, K., Dong, S., Luo, G., Zhang, X., Yang, T., Gao, X., et al. (2025) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1013050 · Cited by 8

Analysis of thymic generation of shared T‐cell receptor α repertoire associated with recognition of tumor antigens shows no preference for neoantigens over wild‐type antigens

Mattila, J., Sormunen, S., Heikkilä, N., Mattila, I. P., Saramäki, J., & Arstila, T. P. (2023) · Cancer Medicine · doi:10.1002/cam4.6002 · Cited by 8

TSpred: a robust prediction framework for TCR–epitope interactions using paired chain TCR sequence data

Kim, H. Y., Kim, S., Park, W., & Kim, D. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae472 · Cited by 7

Long-term survival without graft-versus-host-disease following infusion of allogeneic myeloma-specific Vβ T cell families

Yado, S., Luboshits, G., Hazan, O., Or, R., & Firer, M. A. (2019) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-019-0776-9 · Cited by 7

High-Throughput T Cell Receptor Sequencing Reveals Differential Immune Repertoires in Autoimmune Thyroid Disease

Jia, X., Zhai, T., Wang, B., Yao, Q., Zhang, J.-A., & 宋, 荣. (2019) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2022.111644 · Cited by 8

GGNpTCR: A Generative Graph Structure Neural Network for Predicting Immunogenic Peptides for T-cell Immune Response

Zhao, M., Xu, S. X., Yang, Y., & Yuan, M. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01293 · Cited by 8

An altered HLA-A0201-restricted MUC1 epitope that could induce more efficient anti-tumor effects against gastric cancer

Yu, H., Ye, C., Li, J., Pan, C., Lin, W., Chen, H., Zhou, Z., & Ye, Y. (2020) · Experimental Cell Research · doi:10.1016/j.yexcr.2020.111953 · Cited by 7

Altered HLA‐A2‐restricted TP53 epitope induces specific CTL cytotoxicity against hepatocellular carcinoma

Ye, C., Lin, S., Hong, J., Liu, F., Guo, G., Chen, S., Zhou, Z., Lin, W., Li, J., & Ye, Y. (2023) · European Journal of Immunology · doi:10.1002/eji.202250054 · Cited by 7

Detection of hepatitis B virus DNA in human serum based on highly sensitive electrochemical sensor

Wu, Y. Y., Li, N., Xu, S., Chong, X., & Zhang, C. L. (2022) · International Journal of Electrochemical Science · doi:10.20964/2022.09.26 · Cited by 6

Immunomagnetic cell sorting

Legut, M., & Sanjana, N. E. (2019) · Nature Biomedical Engineering · doi:10.1038/s41551-019-0459-3 · Cited by 6

Monitoring islet specific immune responses in type 1 diabetes clinical immunotherapy trials

Arif, S., Domingo‐Vila, C., Pollock, E., Christakou, E., Williams, E., & Tree, T. I. M. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1183909 · Cited by 6

A Biologically Informed Vision‐Guided Framework for Interpretable T Cell Receptor–Epitope Binding Prediction

Yuan, Y., Chen, J., Zhang, Y., Fang, Y., Fang, Z., Chu, Y., Li, J., Zhang, C., Li, Y., & Wei, D. (2025) · Advanced Science · doi:10.1002/advs.202512544 · Cited by 5

LightCTL: lightweight contrastive TCR-pMHC specificity learning with context-aware prompt

Ye, F., Chen, M., Huang, Y., Zhang, R., Li, X., Wang, X., Han, S., Ma, L., & Liu, X. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf246 · Cited by 5

Deciphering Membrane‐Protein Interactions and High‐Throughput Antigen Identification with Cell Doublets

Wang, Y., Wang, Z., Yang, J., Lei, X., Liu, Y., Frankiw, L., Wang, J., & Li, G. (2024) · Advanced Science · doi:10.1002/advs.202305750 · Cited by 4

Methods to edit T cells for cancer immunotherapy

Lucibello, F., Menegatti, S., & Menger, L. (2019) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2019.05.048 · Cited by 5

Rapid TCR:Epitope Ranker (RAPTER): a primary human T cell reactivity screening assay pairing epitope and TCR at single cell resolution

Deering, R. P., Blumenberg, L. M., Li, L., Dhanik, A., Jeong, S., Pourpe, S., Song, H., Boucher, L., Ragunathan, S., Li, Y., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-35710-7 · Cited by 5

Cross-competition shapes CD8+ T cell hierarchies and differentiation after RNA vaccinationPreprint

McCarron, M. J., Hornburg, M., Wu, T. D., Tong, A.-J., Tähtinen, S., Darwish, M., Freund, E. C., Feng, Y., Eisel, D., Balança, C.-C., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.26.684631 · Cited by 5

DNA Origami Scaffold-Based Peptide-Major Histocompatibility Complex Multimers for Spatial Imaging of T Cells

Wang, J., Yang, H., Chen, J., Sun, Y., Pei, H., & Li, L. (2025) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.5c00383 · Cited by 4

Pretraining Transformers for TCR-pMHC Binding Prediction

Shang, J., Jiao, Q., Chen, C., Zhu, D., & Cui, X. (2022) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm55620.2022.9994875 · Cited by 4

Antigen discovery tools for adaptive immune receptor repertoire research

Bousbaine, D., & Ploegh, H. L. (2020) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2020.10.002 · Cited by 4

CRISPR-targeted display of functional T cell receptors enables engineering of enhanced specificity and prediction of cross-reactivityPreprint

Vazquez-Lombardi, R., Jung, J. S., Bieberich, F., Kapetanovic, E., Aznauryan, E. I., Weber, C. R., & Reddy, S. T. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.23.166363 · Cited by 4

Defining T cell receptor repertoires using nanovial-based affinity and functional screeningPreprint

Koo, D., Mao, Z., Dimatteo, R., Tsubamoto, N., Noguchi, M., McLaughlin, J., Tran, W., Lee, S., Cheng, D., de Rutte, J. M., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.17.524440 · Cited by 4

TCRfinder: Improved TCR virtual screening for novel antigenic peptides with tailored language modelsPreprint

Li, Y., Zhang, C., Zhang, X., & Zhang, Y. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.27.601008 · Cited by 4

ITRAP2, a flexible and robust strategy to assign antigen recognition of T-cells in coupled single-cell TCR-pMHC assayPreprint

Nos, G., Bentzen, A. K., Viuff, M. C., Johansen, K. H., Nilsson, J. B., Kristensen, N. P., Carstensen, L. S., Voss, L. F., Kadivar, M., Nielsen, M., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.19.695506 · Cited by 4

Pre-existing T Cell Memory to Novel Pathogens

Afroz, S., Bartolo, L., & Su, L. F. (2023) · ImmunoHorizons · doi:10.4049/immunohorizons.2200003 · Cited by 3

In Vivo Time-Resolved Single-Cell RNA-Seq Reveals Chemotherapy-Induced Transcriptional Dynamics in Tumor Infiltrating Lymphocytes

Zhu, W., Wu, X., Zhao, Z., Zhou, M. R., Zhang, T., Zhao, D., Jiang, N., Yang, X., Guo, H., Fang, N., et al. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.4c05648 · Cited by 3

Strategies for HIV-1 suppression through key genes and cell therapy

Sorokina, A. V., Anchakova, E., & Dashinimaev, E. B. (2023) · Frontiers in Medicine · doi:10.3389/fmed.2023.1259995 · Cited by 4

Pep2TCR: Accurate prediction of CD4 T cell receptor binding specificity through transfer learning and ensemble approach

Diao, K., Wu, T., Zhao, X., Wang, N., Qiu, D., Wang, W., Li, X., & Liu, X. (2024) · iMetaOmics. · doi:10.1002/imo2.43 · Cited by 3

Comprehensive analysis of antiviral adaptive immunity formation and reactivation down to single-cell levelPreprint

Minervina, A. A., Pogorelyy, M. V., Komech, E. A., Karnaukhov, V. K., Bächer, P., Rosati, E., Franke, A., Chudakov, D. M., Mamedov, I. Z., Lebedev, Y. B., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/820134 · Cited by 3

ATRAP - Accurate T cell Receptor Antigen Pairing through data-driven filtering of sequencing information from single-cellsPreprint

Povlsen, H. R., Bentzen, A. K., Kadivar, M., Jessen, L. E., Hadrup, S. R., & Nielsen, M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.31.506001 · Cited by 3

Neo-epitope identification by weakly-supervised peptide-TCR binding predictionPreprint

Gao, Y., Gao, Y., Li, W., Wu, S., Xing, F., Zhou, C., Fu, S., Chuai, G., Chen, Q., Zhang, H., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.02.550128 · Cited by 3

Characterization of human CMV-specific CD8+ T cells using multi-layer single-cell omics

Gemünd, I. D., Bonaguro, L., Becker, M., Müller, S. M., Joos, C., Domenico, E. D., Aschenbrenner, A. C., Schultze, J. L., Moosmann, A., & Beyer, M. (2025) · Cell Reports Methods · doi:10.1016/j.crmeth.2025.101085 · Cited by 2

TCR representation learning with protein language models: a comprehensive review

Kinoshita, K., & Kobayashi, T. J. (2025) · International Immunology · doi:10.1093/intimm/dxaf048 · Cited by 3

Weakly supervised peptide-TCR binding prediction facilitates neoantigen identification

Gao, Y., Gao, Y., Wu, S., Li, D., Zhou, C., Meng, F., Dong, K., Zhao, X., Li, P., Liang, A., et al. (2025) · Cell Systems · doi:10.1016/j.cels.2025.101403 · Cited by 7

Single-cell protein profiling energized by microfluidic technology

Yang, R., Ruan, Q., Guo, W., Shen, H., Lin, X., Chen, Y., Tao, Y., Yang, C. J., & Ren, Y. (2026) · Lab on a Chip · doi:10.1039/d5lc00854a · Cited by 2

Breaking the deadlock in antigen discovery for Leishmania vaccines

Adriaensen, W. J., de Vrij, N., Pham, T., Laukens, K., Meysman, P., & Kaye, P. M. (2026) · Trends in Parasitology · doi:10.1016/j.pt.2026.01.005 · Cited by 2

Tetramer-Associated T Cell Receptor Sequencing

Malone, M. D., Ma, K.-Y., Zhang, S., & Jiang, N. J. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2712-9_8 · Cited by 2

In silico specificity determination of neoantigen-reactive T-lymphocytes

Kniga, A. E., Polyakov, I. V., & Nemukhin, A. V. (2021) · Biomeditsinskaya Khimiya · doi:10.18097/pbmc20216703251 · Cited by 2

Residue substitution enhances the immunogenicity of neoepitopes from gastric cancers

Yu, H., Li, J., Yuan, Y., Chen, Y., Hong, J., Ye, C., Lin, W., Chen, H., Guo, Z., Li, B., et al. (2021) · Cancer Biology and Medicine · doi:10.20892/j.issn.2095-3941.2021.0022 · Cited by 2

Single Cell Multiomic Approaches to Disentangle T Cell Heterogeneity

Abondio, P., Intinis, C. D., Júnior, J. L. D. S. G. V., & Pace, L. (2022) · Immunology Letters · doi:10.1016/j.imlet.2022.04.008 · Cited by 2

Multimodal T Cell Analysis with CoNGA

Schattgen, S., Hazelton, W. D., Thomas, P. G., & Bradley, P. H. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2712-9_17 · Cited by 2

The myriad targets of a T cell

Natarajan, A., & Krogsgaard, M. (2018) · Nature Biotechnology · doi:10.1038/nbt.4309 · Cited by 2

Preface: More than two decades of modern tumor immunology

Galluzzi, L., & Rudqvist, N.-P. (2020) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(20)30020-3 · Cited by 2

Structure-activity mapping of the peptide- and force-dependent landscape of T-cell activationPreprint

Feng, Y., Zhao, X., White, A. K., García, K. C., & Fordyce, P. M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.24.441194 · Cited by 2

TSpred: a robust prediction framework for TCR-epitope interactions based on an ensemble deep learning approach using paired chain TCR sequence dataPreprint

Kim, H. Y., Kim, S., Park, W., & Kim, D. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.04.570002 · Cited by 2

T-cell receptor specificity landscape revealed through de novo peptide designPreprint

Visani, G. M., Pun, M. N., Minervina, A. A., Bradley, P., Thomas, P., & Nourmohammad, A. (2025) · bioRxiv · doi:10.1101/2025.02.28.640903 · Cited by 6

General prediction of T cell receptor antigen specificity from sequence using AlphaFold 3

Woods, L., Neff, B., Lahouel, K., Goursaud, A., Mulazimoglu, M., Bates, K., Tomasetti, C., & Altin, J. A. (2026) · Science Advances · doi:10.64898/2026.06.02.729478 · Cited by 2

Ready-to-load MHC-I nanoparticles for high-throughput T cell screening studies

Phan, H. A. T., Eom, S., Hwang, D., Young, M. C., Sun, S. M., Erdman, M. C., Sun, Y., Mallik, L., Rotsides, P., Painter, M. M., et al. (2026) · Science Advances · doi:10.1126/sciadv.adv2687 · Cited by 1

DapPep: Domain Adaptive Peptide-agnostic Learning for Universal T-cell Receptor-antigen Binding Affinity Prediction

Zheng, J., Xu, Q., Xia, R., & Li, S. Z. (2025) · IEEE International Conference on Acoustics Speech and Signal Processing · doi:10.1109/icassp49660.2025.10888436 · Cited by 1

Novel methods for the discovery of disease-associated T cell epitopes in autoimmunity

Mertens, E. J., Willekens, B. M. P., Derdelinckx, J., & Cools, N. (2026) · Methods · doi:10.1016/j.ymeth.2026.02.004 · Cited by 2

AI-driven computational methods and benchmarking for T-cell antigen identification

Deng, Y., Que, J., Xue, G., Cai, Y., Yang, W., Wang, Y., Yi, H., Wang, Z., Lin, Y., Zhou, W., et al. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag123 · Cited by 1

The adaptive immune receptors in a big data world

DeKosky, B. J. (2026) · ImmunoHorizons · doi:10.1093/immhor/vlaf081 · Cited by 1

Identification of T cell antigens in the 21st century, as difficult as ever

Lantz, O. J., & Teyton, L. (2022) · Seminars in Immunology · doi:10.1016/j.smim.2022.101659 · Cited by 1

Phenotypic screening of signaling motifs that efficiently induce cell proliferation

Umene, K., Nagamune, T., & Kawahara, M. (2023) · Scientific Reports · doi:10.1038/s41598-023-42378-6 · Cited by 1

Construction and efficacy testing of DNA vaccines containing HLA-A*02:01-restricted SARS-CoV-2 T-cell epitopes predicted by immunoinformatics

Tan, D., Kang, N., Zhu, Y., Hou, J., Wang, H., Xu, H., Zu, C., Gao, Z., Liu, M., Liu, N., et al. (2024) · Acta Biochimica et Biophysica Sinica · doi:10.3724/abbs.2024039 · Cited by 1

Systematic discovery of receptor-ligand biology by engineered cell entry and single-cell genomicsPreprint

Yu, B., Shi, Q., Belk, J. A., Yost, K. E., Parker, K. R., Huang, H., Lingwood, D., Davis, M. M., Satpathy, A. T., & Chang, H. Y. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.13.472464 · Cited by 1

Preface: More than two decades of modern tumor immunology

Galluzzi, L., & Rudqvist, N.-P. (2019) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(19)30459-8 · Cited by 1

Preface: More than two decades of modern tumor immunology

Galluzzi, L., & Rudqvist, N.-P. (2020) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(20)30043-4 · Cited by 1

DextraDemixer enables accurate identification of antigen-specific T cells from pMHC multimer experimentsPreprint

岸, 洋., Drost, F., Bonafonte-Pardàs, I., Grotz, M., Schober, K., & Schubert, B. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.23.733339 · Cited by 1

Preface: More than two decades of modern tumor immunology

Galluzzi, L., & Rudqvist, N.-P. (2020) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(20)30077-x

Preface: More than two decades of modern tumor immunology

Galluzzi, L., & Rudqvist, N.-P. (2020) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(20)30114-2

Antigen-specific T cells

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Faculty Opinions recommendation of T-Scan: A Genome-wide Method for the Systematic Discovery of T Cell Epitopes.

Dustin, M. L., & Mayya, V. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.736361281.793566682

Predicting TCR sequences for unseen antigen epitopes using structural and sequence featuresPreprint

Zhang, H., Ji, H., Zhang, C., & Zhang, Q. (2024) · Research Square · doi:10.21203/rs.3.rs-3891946/v1

Beyond Single Clones: High-Throughput Sequencing in Antibody DiscoveryPreprint

Fahad, A. S., Gutiérrez-González, M., Madan, B., & DeKosky, B. J. (2024) · Cold Spring Harbor Protocols · doi:10.1101/pdb.top107772

Microfluidic‐Enabled Production of DNA Barcoded APC Library (MEDAL) for High Throughput T Cell Epitope Screening

Cui, X., Liu, Y., Wu, T., Tay, M. Z., & Cheow, L. F. (2025) · Small Methods · doi:10.1002/smtd.202500150

HLA-DQ monomer-based enrichment of alloreactive CD4 T cellsPreprint

Zhanzak, Z., Cina, D., Zhang, X., Hadley, A., Kissick, H. T., & Larsen, C. P. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.30.656890

Modern Laboratory Test-Systems as Platforms for Validation of Clinically Promising T-Cell Receptors

Mungalov, R. V., Vand, N. S., Chudakov, D. M., & Bryushkova, E. A. (2025) · Russian Journal of Bioorganic Chemistry · doi:10.1134/s1068162025601910

Disrupting explicit encoding paradigms: property-interactive transformers decode T-cell receptor specificity beyond dataset biases

Yang, L., Liu, H. H., Calanche, A., Gokcek, S. M., Singh, V., Sansoterra, N., Akkaya, M., Akkaya, B., & Yılmaz, A. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf609

Experimental immunologists in the era of artificial intelligence

Wang, Y., Ouyang, W. O., Wang, C., Nourmohammad, A., Liu, G., & Wu, N. C. (2026) · Trends in Immunology · doi:10.1016/j.it.2026.01.003

Development and characterization of novel T-cell receptor–like antibodies targeting human papillomavirus type 16 oncoprotein peptides for early cervical cancer detection using experimental and computational approaches

Sachit, B. A., Dass, S. A., Rajan, R. S., Tye, G. J., & Balakrishnan, V. (2026) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2026.152755

Generative design of antigen-specific T-cell receptor sequences with a conditional diffusion modelPreprint

Zhang, Y., Liang, W., 许舒婷, Witney, M. J., Su, X., Andrews, M. C., Rossjohn, J., Purcell, A. W., Wang, F., & Song, J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.10.730756

Computational prediction of TCR cross-reactivity: principles, challenges and translational opportunities

Li, W., Pan, Y. P., Wu, X., Song, Y., Wang, Y., & Xie, L. (2026) · Journal of Translational Medicine · doi:10.1186/s12967-026-08476-5

Physics-informed deep learning: A new paradigm for macromolecular recognition and rational protein design

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(Single-cell omics) Single-cell TCR-sequence

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OmniTCR: a foundation model unifying T cell receptor recognition prediction and conditional sequence generationPreprint

Zeng, F., Feng, D., Song, D., Ding, L., Tan, Z., Lei, Q., Lei, W., & Guo, A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.10.750588

Discovery of rare antigen-specific TCRs via replicate profiling

Egorov, E. S., Kriukova, V., Шагина, И. А., Sharonov, G. V., Lupyr, K., Staroverov, D. B., Lukyanov, D. K., Salnikova, M. A., Nikolaev, R. V., Shelikhova, L., et al. (2026) · Scientific Reports · doi:10.1038/s41598-026-71520-3

Discovery of Post‐Translationally Modified Epitopes in Autoimmunity: Someone Has to Fish so Everyone Can Eat

Arshad, S., Cameron, B. M., & Joglekar, A. V. (2026) · Immunological Reviews · doi:10.1111/imr.70179

T cell immunomonitoring: a comparative analysis of traditional and novel methods to quantify and characterize human antigen-specific T cells

Lazzaro, S., Leroux-Roels, G. G., Janetzki, S., Salaun, B., Cook, L. E., Franke, K., Poschke, I. C., Bunse, L., Welters, M. J. P., Fehlings, M., et al. (2026) · Nature Protocols · doi:10.1038/s41596-026-01453-8 · Cited by 1

T cell receptor-engineered T cells for hepatocellular carcinoma: next steps and future perspectives

Li, Z., Shu, J., Zhang, Q., Su, S., Zhou, J., Luan, Y., Xu, J., Gu, J., & Huang, X. (2026) · Clinical Cancer Bulletin · doi:10.1007/s44272-026-00075-1

Single-cell Transcriptomics in Autoimmune Diseases: Mechanistic Insights, Cross-disease Convergence, and Translational Challenges in Rheumatoid Arthritis, Systemic Lupus Erythematosus, Type 1 Diabetes, and Multiple Sclerosis

Nguyen, T.-H., Nguyen, T.-D., Hoang, O.-T., Can, T.-T. T., Nguyen, M.-H. T., Tran, M.-H., Chu, H.-C., & Nguyen, D.-V. (2026) · Clinical Reviews in Allergy & Immunology · doi:10.1007/s12016-026-09211-0

High-throughput single-cell linking of antigen specificities with T cell receptor sequences using de novo generated DNA-linked MHC tetramers

Jiang, N. J. (2018) · The Journal of Immunology · doi:10.4049/jimmunol.200.supp.120.23

Abstract 4678: High-throughput single-cell linking of antigen specificities with T cell receptor sequences using de novo generated DNA-linked MHC tetramers

Jiang, N. J., Zhang, S., He, C., Sun, E., Zhang, M., & Jia, W. (2018) · Cancer Research · doi:10.1158/1538-7445.am2018-4678

Direct identification of neoantigen-specific TCRs from tumor specimens by high-throughput single-cell sequencing

Lu, Y., Zheng, Z., Lowery, F. J., Gartner, J. J., Prickett, T. D., Robbins, P. F., & Rosenberg, S. A. (2021) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2021-002595 · Cited by 63

Tetramer-Associated T Cell Receptor Sequencing

Malone, M. D., Ma, K.-Y., Zhang, S., & Jiang, N. J. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2712-9_8 · Cited by 2

Abstract 4066: High throughput single-cell TCR sequencing method identifies cancer-specific TCR clonotypes

Papalexi, E., Curca, C., Hariadi, B., Suyama, A., Marrujo, S. R., Geiss, G. K., Roco, C. M., & Rosenberg, A. (2025) · Cancer Research · doi:10.1158/1538-7445.am2025-4066