T‐cell receptor and B‐cell receptor repertoire profiling in adaptive immunity

PD-1 blockade induces responses by inhibiting adaptive immune resistance

Tumeh, P. C., Harview, C. L., Yearley, J. H., Shintaku, I. P., Taylor, E. J. M., Robert, L., Chmielowski, B., Spasic, M., Henry, G., Ciobanu, V., et al. (2014) · Nature · doi:10.1038/nature13954 · Cited by 6,609 · see citing works

Neoadjuvant PD-1 Blockade in Resectable Lung Cancer

Forde, P. M., Chaft, J. E., Smith, K. N., Anagnostou, V., Cottrell, T. R., Hellmann, M. D., Zahurak, M., Yang, S. C., Jones, D. R., Broderick, S., et al. (2018) · New England Journal of Medicine · doi:10.1056/nejmoa1716078 · Cited by 2,099 · see citing works

MiXCR: software for comprehensive adaptive immunity profiling

Bolotin, D. A., Poslavskii, S., Mitrophanov, I., Shugay, M., Mamedov, I. Z., Putintseva, E. V., & Chudakov, D. M. (2015) · Nature Methods · doi:10.1038/nmeth.3364 · Cited by 1,730 · see citing works

Comprehensive assessment of T-cell receptor β-chain diversity in αβ T cells

Robins, H. S., Campregher, P. V., Srivastava, S. K., Wacher, A., Turtle, C. J., Kahsai, O., Riddell, S. R., Warren, E. H., & Carlson, C. S. (2009) · Blood · doi:10.1182/blood-2009-04-217604 · Cited by 1,122 · see citing works

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 · see citing works

Counting absolute numbers of molecules using unique molecular identifiers

Kivioja, T., Vähärautio, A., Karlsson, K., Bonke, M., Enge, M., Linnarsson, S., & Taipale, J. (2012) · Nature Methods · doi:10.1038/nmeth.1778 · Cited by 1,010 · see citing works

Quantifiable predictive features define epitope-specific T cell receptor repertoires

Dash, P., Fiore-Gartland, A. J., Hertz, T., Wang, G., Sharma, S., Souquette, A. H., Crawford, J. C., Clemens, E. B., Nguyen, T. H. O., Kedzierska, K., et al. (2017) · Nature · doi:10.1038/nature22383 · Cited by 886 · see citing works

Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance

Roh, W., Chen, P.-L., Reuben, A., Spencer, C. N., Prieto, P. A., Miller, J. P., Gopalakrishnan, V., Wang, F., Cooper, Z. A., Reddy, S. M., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aah3560 · Cited by 859 · see citing works

Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients

Gros, A., Parkhurst, M. R., Tran, E., Pasetto, A., Robbins, P. F., Ilyas, S., Prickett, T. D., Gartner, J. J., Crystal, J. S., Roberts, I. M., et al. (2016) · Nature Medicine · doi:10.1038/nm.4051 · Cited by 830 · see citing works

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity

Shugay, M., Bagaev, D. V., Zvyagin, I. V., Vroomans, R. M. A., Crawford, J. C., Dolton, G. M., Komech, E. A., Sycheva, A. L., Koneva, A. E., Egorov, E. S., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx760 · Cited by 623 · see citing works

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

Shugay, M., Bagaev, D. V., Turchaninova, M. A., Bolotin, D. A., Britanova, O. V., Putintseva, E. V., Pogorelyy, M. V., Nazarov, V. I., Zvyagin, I. V., Kirgizova, V., et al. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004503 · Cited by 608 · see citing works

Human Effector and Memory CD8+ T Cell Responses to Smallpox and Yellow Fever Vaccines

Miller, J. D., van der Most, R. G., Akondy, R. S., Glidewell, J. T., Albott, S., Masopust, D., Murali-Krishna, K., Mahar, P. L., Edupuganti, S., Lalor, S., et al. (2008) · Immunity · doi:10.1016/j.immuni.2008.02.020 · Cited by 601 · see citing works

Using synthetic templates to design an unbiased multiplex PCR assay

Carlson, C. S., Emerson, R., Sherwood, A., Desmarais, C., Chung, M., Parsons, J. M., Steen, M. S., LaMadrid-Herrmannfeldt, M., Williamson, D. W., Livingston, R. J., et al. (2013) · Nature Communications · doi:10.1038/ncomms3680 · Cited by 568 · see citing works

McPAS-TCR: a manually curated catalogue of pathology-associated T cell receptor sequences

Tickotsky, N., Sagiv, T., Prilusky, J., Shifrut, E., & Friedman, N. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx286 · Cited by 560 · see citing works

Immunoglobulin Analysis Tool: A Novel Tool for the Analysis of Human and Mouse Heavy and Light Chain Transcripts

Rogosch, T., Kerzel, S., Hoi, K. H., Zhang, Z., Maier, R. F., Ippolito, G. C., & Zemlin, M. (2012) · Frontiers in Immunology · doi:10.3389/fimmu.2012.00176 · Cited by 555 · see citing works

Commonality despite exceptional diversity in the baseline human antibody repertoire

Briney, B., Inderbitzin, A., Joyce, C., & Burton, D. R. (2019) · Nature · doi:10.1038/s41586-019-0879-y · Cited by 544 · see citing works

Linking T-cell receptor sequence to functional phenotype at the single-cell level

Han, A. S., Glanville, J., Hansmann, L., & Davis, M. M. (2014) · Nature Biotechnology · doi:10.1038/nbt.2938 · Cited by 534 · see citing works

Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire

Emerson, R. O., DeWitt, W. S., Vignali, M., Gravley, J., Hu, J. K., Osborne, E. J., Desmarais, C., Klinger, M., Carlson, C. S., Hansen, J. A., et al. (2017) · Nature Genetics · doi:10.1038/ng.3822 · Cited by 532 · see citing works

Estimating Population Size Via Sample Coverage for Closed Capture-Recapture Models

Lee, S., & Chao, A. (1994) · Biometrics · doi:10.2307/2533199 · Cited by 493 · see citing works

T cell fate and clonality inference from single-cell transcriptomes

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Towards error-free profiling of immune repertoires

Shugay, M., Britanova, O. V., Merzlyak, E. M., Turchaninova, M. A., Mamedov, I. Z., Tuganbaev, T., Bolotin, D. A., Staroverov, D. B., Putintseva, E. V., Plevová, K., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2960 · Cited by 428 · see citing works

High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire

DeKosky, B. J., Ippolito, G. C., Deschner, R. P., Lavinder, J. J., Wine, Y., Rawlings, B. M., Varadarajan, N., Giesecke, C., Dörner, T., Andrews, S. F., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2492 · Cited by 410 · see citing works

Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencingPreprint

Freeman, J., Warren, R. M., Webb, J. R., Nelson, B. H., & Holt, R. A. (2009) · Genome Research · doi:10.1101/gr.092924.109 · Cited by 385 · see citing works

Amplification of cDNA ends based on template-switching effect and step- out PCR

Matz, M. V. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.6.1558 · Cited by 380 · see citing works

Structural determinants of T-cell receptor bias in immunity

Turner, S. J., Doherty, P. C., McCluskey, J., & Rossjohn, J. (2006) · Nature reviews. Immunology · doi:10.1038/nri1977 · Cited by 373 · see citing works

CTLA4 Blockade Broadens the Peripheral T-Cell Receptor Repertoire

Robert, L., Tsoi, J., Wang, X., Emerson, R., Homet, B., Chodon, T., Mok, S., Huang, R., Cochran, A. J., Comı́n-Anduix, B., et al. (2014) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-13-2648 · Cited by 373 · see citing works

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs

Parekh, S., Ziegenhain, C., Vieth, B., Enard, W., & Hellmann, I. (2018) · GigaScience · doi:10.1093/gigascience/giy059 · Cited by 349 · see citing works

The Yellow Fever Virus Vaccine Induces a Broad and Polyfunctional Human Memory CD8+ T Cell Response

Akondy, R. S., Monson, N. D., Miller, J. D., Edupuganti, S., Teuwen, D. E., Wu, H. G., Quyyumi, F. F., Garg, S., Altman, J. D., del Rı́o, C., et al. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0803903 · Cited by 345 · see citing works

T cells in patients with narcolepsy target self-antigens of hypocretin neurons

Latorre, D., Kallweit, U., Armentani, E., Foglierini, M., Mele, F., Cassotta, A., Jovic, S., Jarrossay, D., Mathis, J., Zellini, F., et al. (2018) · Nature · doi:10.1038/s41586-018-0540-1 · Cited by 334 · see citing works

Overview of methodologies for T-cell receptor repertoire analysis

Rosati, E., Dowds, C. M., Liaskou, E., Henriksen, E. K. K., Karlsen, T. H., & Franke, A. (2017) · BMC Biotechnology · doi:10.1186/s12896-017-0379-9 · Cited by 322 · see citing works

Antigen receptor repertoire profiling from RNA-seq data

Bolotin, D. A., Poslavskii, S., Davydov, A. N., Frenkel, F. E., Fanchi, L. F., Zolotareva, O. I., Hemmers, S., Putintseva, E. V., Obraztsova, A., Shugay, M., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3979 · Cited by 318 · see citing works

Statistical inference of the generation probability of T-cell receptors from sequence repertoires

Murugan, A., Mora, T., Walczak, A. M., & Callan, C. G. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1212755109 · Cited by 292 · see citing works

Clinically resolved psoriatic lesions contain psoriasis-specific IL-17–producing αβ T cell clones

Matos, T. R., O’Malley, J. T., Lowry, E. L., Hamm, D. E., Kirsch, I. R., Robins, H. S., Kupper, T. S., Krueger, J. G., & Clark, R. A. (2017) · Journal of Clinical Investigation · doi:10.1172/jci93396 · Cited by 286 · see citing works

Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination

Lee, J., Boutz, D. R., Chromikova, V., Joyce, M. G., Vollmers, C., Leung, K., Horton, A. P., DeKosky, B. J., Lee, C., Lavinder, J. J., et al. (2016) · Nature Medicine · doi:10.1038/nm.4224 · Cited by 278 · see citing works

Convergent Antibody Signatures in Human Dengue

Parameswaran, P., Liu, Y., Roskin, K. M., Jackson, K., Dixit, V. P., Lee, J.-Y., Artiles, K. L., Zompì, S., Vargas, M. J., Simen, B. B., et al. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.05.008 · Cited by 261 · see citing works

T cell repertoire following autologous stem cell transplantation for multiple sclerosis

Muraro, P. A., Robins, H. S., Malhotra, S., Howell, M., Phippard, D., Desmarais, C., Sousa, A. D. P. A., Griffith, L. M., Lim, N., Nash, R. A., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci71691 · Cited by 256 · see citing works

Human Responses to Influenza Vaccination Show Seroconversion Signatures and Convergent Antibody Rearrangements

Jackson, K., Liu, Y., Roskin, K. M., Glanville, J., Hoh, R. A., Seo, K., Marshall, E. L., Gurley, T. C., Moody, M. A., Haynes, B. F., et al. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.05.013 · Cited by 251 · see citing works

High-throughput immune repertoire analysis with IGoR

Marcou, Q., Mora, T., & Walczak, A. M. (2018) · Nature Communications · doi:10.1038/s41467-018-02832-w · Cited by 245 · see citing works

Immune Toxicities Elicted by CTLA-4 Blockade in Cancer Patients Are Associated with Early Diversification of the T-cell Repertoire

Oh, D. Y., Cham, J., Zhang, L., Fong, G., Kwek, S. S., Klinger, M., Faham, M., & Fong, L. (2017) · Cancer Research · doi:10.1158/0008-5472.can-16-2324 · Cited by 236 · see citing works

Tracking donor-reactive T cells: Evidence for clonal deletion in tolerant kidney transplant patients

Morris, H. K., DeWolf, S., Robins, H. S., Sprangers, B., LoCascio, S. A., Shonts, B. A., Kawai, T., Wong, W., Yang, S., Zuber, J., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.3010760 · Cited by 231 · see citing works

Allogeneic Stem Cell Transplantation: A Historical and Scientific Overview

Singh, A. K., & McGuirk, J. P. (2016) · Cancer Research · doi:10.1158/0008-5472.can-16-1311 · Cited by 231 · see citing works

OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs

Sethna, Z. M., Elhanati, Y., Callan, C. G., Walczak, A. M., & Mora, T. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz035 · Cited by 227 · see citing works

Clonal expansion of CD8 T cells in the systemic circulation precedes development of ipilimumab-induced toxicities

Subudhi, S. K., Aparicio, A., Gao, J., Zurita, A. J., Araujo, J. C., Logothetis, C. J., Tahir, S. A., Korivi, B. R., Slack, R. S., Vence, L., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1611421113 · Cited by 226 · see citing works

tcR: an R package for T cell receptor repertoire advanced data analysis

Nazarov, V. I., Pogorelyy, M. V., Komech, E. A., Zvyagin, I. V., Bolotin, D. A., Shugay, M., Chudakov, D. M., Lebedev, Y. B., & Mamedov, I. Z. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0613-1 · Cited by 223 · see citing works

Quantitative assessment of T cell repertoire recovery after hematopoietic stem cell transplantation

van Heijst, J. W. J., Ceberio, I., Lipuma, L., Samilo, D., Wasilewski, G., Gonzales, A. M., Nieves, J., van den Brink, M. R. M., Perales, M., & Pamer, E. G. (2013) · Nature Medicine · doi:10.1038/nm.3100 · Cited by 206 · see citing works

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

Zhang, S.-Q., Ma, K.-Y., Schonnesen, A. A., Zhang, M., He, C., Sun, E., Williams, C. M., Jia, W., & Jiang, N. (2018) · Nature Biotechnology · doi:10.1038/nbt.4282 · Cited by 200 · see citing works

Tumor-infiltrating human CD4 + regulatory T cells display a distinct TCR repertoire and exhibit tumor and neoantigen reactivity

Ahmadzadeh, M., Pasetto, A., Jia, L., Deniger, D. C., Stevanović, S., Robbins, P. F., & Rosenberg, S. A. (2019) · Science Immunology · doi:10.1126/sciimmunol.aao4310 · Cited by 198 · see citing works

Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires

Miho, E., Yermanos, A., Weber, C. R., Berger, C. T., Reddy, S. T., & Greiff, V. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.00224 · Cited by 189 · see citing works

High-quality full-length immunoglobulin profiling with unique molecular barcoding

Turchaninova, M. A., Davydov, A., Britanova, O. V., Shugay, M., Bikos, V., Egorov, E. S., Kirgizova, V., Merzlyak, E. M., Staroverov, D. B., Bolotin, D. A., et al. (2016) · Nature Protocols · doi:10.1038/nprot.2016.093 · Cited by 178 · see citing works

High-throughput identification of antigen-specific TCRs by TCR gene capture

Linnemann, C., Heemskerk, B., Kvistborg, P., Kluin, R. J. C., Bolotin, D. A., Chen, X. T., Bresser, K., Nieuwland, M., Schotte, R., Michels, S., et al. (2013) · Nature Medicine · doi:10.1038/nm.3359 · Cited by 177 · see citing works

A Mechanism for TCR Sharing between T Cell Subsets and Individuals Revealed by Pyrosequencing

Venturi, V., Quigley, M. F., Greenaway, H. Y., Ng, P. C., Ende, Z. S., McIntosh, T. C., Asher, T. E., Almeida, J. R., Levy, S., Price, D. A., et al. (2011) · The Journal of Immunology · doi:10.4049/jimmunol.1003898 · Cited by 175 · see citing works

Haematopoietic stem cell transplantation for autoimmune diseases

Swart, J. F., Delemarre, E. M., van Wijk, F., et al. (2017) · Nature Reviews Rheumatology · doi:10.1038/nrrheum.2017.7 · Cited by 175 · see citing works

Preparing Unbiased T-Cell Receptor and Antibody cDNA Libraries for the Deep Next Generation Sequencing Profiling

Mamedov, I. Z., Britanova, O. V., Zvyagin, I. V., Turchaninova, M. A., Bolotin, D. A., Putintseva, E. V., Lebedev, Y. B., & Chudakov, D. M. (2013) · Frontiers in Immunology · doi:10.3389/fimmu.2013.00456 · Cited by 172 · see citing works

An atlas of B-cell clonal distribution in the human body

Meng, W., Zhang, B., Schwartz, G. W., Rosenfeld, A. M., Ren, D., Thome, J. J. C., Carpenter, D. J., Matsuoka, N., Lerner, H., Friedman, A. L., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3942 · Cited by 172 · see citing works

Hematopoietic stem cell transplantation in its 60s: A platform for cellular therapies

Chabannon, C., Kuball, J. H. E., Bondanza, A., Dazzi, F., Pedrazzoli, P., Toubert, A., Ruggeri, A., Fleischhauer, K., & Bonini, C. (2018) · Science Translational Medicine · doi:10.1126/scitranslmed.aap9630 · Cited by 172 · see citing works

CMV reactivation drives posttransplant T-cell reconstitution and results in defects in the underlying TCRβ repertoire

Suessmuth, Y., Mukherjee, R., Watkins, B. K., Koura, D. T., Finstermeier, K., Desmarais, C., Stempora, L., Horan, J., Langston, A. A., Qayed, M. D., et al. (2015) · Blood · doi:10.1182/blood-2015-03-631853 · Cited by 170 · see citing works

A LAIR1 insertion generates broadly reactive antibodies against malaria variant antigens

Tan, J., Pieper, K., Piccoli, L., Abdi, A. I., Foglierini, M., Geiger, R., Tully, C. M., Jarrossay, D., Ndungu, F. M., Wambua, J., et al. (2015) · Nature · doi:10.1038/nature16450 · Cited by 168 · see citing works

Long-term maintenance of human naive T cells through in situ homeostasis in lymphoid tissue sites

Thome, J. J. C., Grinshpun, B., Kumar, B. V., Kubota, M., Ohmura, Y., Lerner, H., Sempowski, G. D., Shen, Y., & Farber, D. L. (2016) · Science Immunology · doi:10.1126/sciimmunol.aah6506 · Cited by 162 · see citing works

Dynamics of the Cytotoxic T Cell Response to a Model of Acute Viral Infection

DeWitt, W. S., Emerson, R., Lindau, P., Vignali, M., Snyder, T. M., Desmarais, C., Sanders, C. M., Utsugi, H., Warren, E. H., McElrath, M. J., et al. (2015) · Journal of Virology · doi:10.1128/jvi.03474-14 · Cited by 161 · see citing works

Single Cell T Cell Receptor Sequencing: Techniques and Future Challenges

Simone, M. C. D., Rossetti, G., & Pagani, M. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.01638 · Cited by 161 · see citing works

Origin and evolution of the T cell repertoire after posttransplantation cyclophosphamide

Kanakry, C. G., Coffey, D. G., Towlerton, A. M. H., Vulic, A., Storer, B. E., Chou, J., Yeung, C. C. S., Gocke, C. D., Robins, H. S., O’Donnell, P. V., et al. (2016) · JCI Insight · doi:10.1172/jci.insight.86252 · Cited by 149 · see citing works

Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity

DeWitt, W. S., Smith, A., Schoch, G. H., Hansen, J. A., Matsen, F. A., IV, & Bradley, P. H. (2018) · eLife · doi:10.7554/elife.38358 · Cited by 149 · see citing works

Next generation sequencing for TCR repertoire profiling: Platform‐specific features and correction algorithms

Bolotin, D. A., Mamedov, I. Z., Britanova, O. V., Zvyagin, I. V., Shagin, D. A., Ustyugova, S. V., Turchaninova, M. A., Lukyanov, S., Lebedev, Y. B., & Chudakov, D. M. (2012) · European Journal of Immunology · doi:10.1002/eji.201242517 · Cited by 147 · see citing works

Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq

Redmond, D., Poran, A., & Elemento, O. (2016) · Genome Medicine · doi:10.1186/s13073-016-0335-7 · Cited by 139 · see citing works

Generation of human memory stem T cells after haploidentical T-replete hematopoietic stem cell transplantation

Cieri, N., Oliveira, G., Greco, R., Forcato, M., Taccioli, C., Cianciotti, B. C., Valtolina, V., Noviello, M., Vago, L., Bondanza, A., et al. (2015) · Blood · doi:10.1182/blood-2014-11-608539 · Cited by 135 · see citing works

Sequence and Structural Analyses Reveal Distinct and Highly Diverse Human CD8+ TCR Repertoires to Immunodominant Viral Antigens

Chen, G., Yang, X., Ko, A., Sun, X., Gao, M., Zhang, Y., Shi, A., Mariuzza, R. A., & Weng, N. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.03.072 · Cited by 132 · see citing works

Pairing of T ‐cell receptor chains via emulsion PCR

Turchaninova, M. A., Britanova, O. V., Bolotin, D. A., Shugay, M., Putintseva, E. V., Staroverov, D. B., Sharonov, G. V., Shcherbo, D. S., Zvyagin, I. V., Mamedov, I. Z., et al. (2013) · European Journal of Immunology · doi:10.1002/eji.201343453 · Cited by 128 · see citing works

Quantitative characterization of T-cell repertoire in allogeneic hematopoietic stem cell transplant recipients

Yew, P., Alachkar, H., Yamaguchi, R., Kiyotani, K., Fang, H., Yap, K. L., Liu, H. T., Wickrema, A., Artz, A. S., van Besien, K., et al. (2015) · Bone Marrow Transplantation · doi:10.1038/bmt.2015.133 · Cited by 125 · see citing works

Predicting the spectrum of TCR repertoire sharing with a data‐driven model of recombination

Elhanati, Y., Sethna, Z., Callan, C. G., Mora, T., & Walczak, A. M. (2018) · Immunological Reviews · doi:10.1111/imr.12665 · Cited by 122 · see citing works

Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins

Pogorelyy, M. V., Minervina, A. A., Touzel, M. P., Sycheva, A. L., Komech, E. A., Kovalenko, E. I., Karganova, G. G., Egorov, E. S., Komkov, A. Y., Chudakov, D. M., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1809642115 · Cited by 122 · see citing works

Single‐cell based high‐throughput sequencing of full‐length immunoglobulin heavy and light chain genes

Busse, C. E., Czogiel, I., Braun, P., Arndt, P. F., & Wardemann, H. (2014) · European Journal of Immunology · doi:10.1002/eji.201343917 · Cited by 121 · see citing works

Advanced Methodologies in High-Throughput Sequencing of Immune Repertoires

Friedensohn, S., Khan, T. A., & Reddy, S. T. (2016) · Trends in biotechnology · doi:10.1016/j.tibtech.2016.09.010 · Cited by 118 · see citing works

Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile

Oakes, T., Heather, J., Best, K., Byng-Maddick, R., Husovsky, C., Ismail, M., Joshi, K., Maxwell, G., Noursadeghi, M., Riddell, N. E., et al. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.01267 · Cited by 116 · see citing works

Discovery of T Cell Receptor β Motifs Specific to HLA–B27–Positive Ankylosing Spondylitis by Deep Repertoire Sequence Analysis

Faham, M., Carlton, V. E. H., Moorhead, M., Zheng, J., Klinger, M., Pepin, F., Asbury, T., Vignali, M., Emerson, R., Robins, H. S., et al. (2016) · Arthritis & Rheumatology · doi:10.1002/art.40028 · Cited by 114 · see citing works

High-resolution analysis of the human T-cell receptor repertoire

Ruggiero, E., Nicolay, J. P., Fronza, R., Arens, A., Paruzynski, A., Nowrouzi, A., Ürenden, G., Lulay, C., Schneider, S. O., Goerdt, S., et al. (2015) · Nature Communications · doi:10.1038/ncomms9081 · Cited by 113 · see citing works

Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires

Greiff, V., Weber, C. R., Palme, J., Bodenhofer, U., Miho, E., Menzel, U., & Reddy, S. T. (2017) · The Journal of Immunology · doi:10.4049/jimmunol.1700594 · Cited by 113 · see citing works

Multi-Donor Longitudinal Antibody Repertoire Sequencing Reveals the Existence of Public Antibody Clonotypes in HIV-1 Infection

Setliff, I., McDonnell, W. J., Raju, N., Bombardi, R. G., Murji, A. A., Scheepers, C., Ziki, R., Mynhardt, C., Shepherd, B. E., Mamchak, A. A., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.05.001 · Cited by 111 · see citing works

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Autologous stem cell transplantation aids autoimmune patients by functional renewal and TCR diversification of regulatory T cells

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Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding

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Public antibodies to malaria antigens generated by two LAIR1 insertion modalities

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Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires

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IMSEQ—a fast and error aware approach to immunogenetic sequence analysis

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Profiling tissue-resident T cell repertoires by RNA sequencing

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Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing

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A new high-throughput sequencing method for determining diversity and similarity of T cell receptor (TCR) α and β repertoires and identifying potential new invariant TCR α chains

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B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle

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Unbiased Molecular Analysis of T Cell Receptor Expression Using Template‐Switch Anchored RT‐PCR

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Ex vivo T-cell depletion in allogeneic hematopoietic stem cell transplant: past, present and future

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In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire

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Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state

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Diversification of the antigen-specific T cell receptor repertoire after varicella zoster vaccination

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Quantification of HTLV-1 Clonality and TCR Diversity

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Early expansion of donor-specific Tregs in tolerant kidney transplant recipients

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T cell receptor repertoire usage in cancer as a surrogate marker for immune responses

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CD8+ T cells with characteristic T cell receptor beta motif are detected in blood and expanded in synovial fluid of ankylosing spondylitis patients

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Method for identification of condition-associated public antigen receptor sequences

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On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition

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Longitudinal analysis of peripheral blood T cell receptor diversity in patients with systemic lupus erythematosus by next-generation sequencing

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High-throughput T cell receptor sequencing identifies clonally expanded CD8+ T cell populations in alopecia areata

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Highly sensitive and unbiased approach for elucidating antibody repertoires

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Tracking the fate and origin of clinically relevant adoptively transferred CD8 + T cells in vivo

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T cell clonal expansions in ileal Crohn’s disease are associated with smoking behaviour and postoperative recurrence

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High Diversity in the TCR Repertoire of GAD65 Autoantigen-Specific Human CD4+ T Cells

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Urine-derived lymphocytes as a non-invasive measure of the bladder tumor immune microenvironment

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Tracking T-cell immune reconstitution after TCRαβ/CD19-depleted hematopoietic cells transplantation in children

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Deep sequencing and human antibody repertoire analysis

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Robust B Cell Responses Predict Rapid Resolution of Lyme Disease

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Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation

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Defining the Alloreactive T Cell Repertoire Using High-Throughput Sequencing of Mixed Lymphocyte Reaction Culture

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Computational Evaluation of B-Cell Clone Sizes in Bulk Populations

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Quantitative characterization of T-cell repertoire and biomarkers in kidney transplant rejection

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CD4+ T Cell-Receptor Repertoire Diversity is Compromised in the Spleen but Not in the Bone Marrow of Aged Mice Due to Private and Sporadic Clonal Expansions

Shifrut, E., Baruch, K., Gal, H., Ndifon, W. O., Deczkowska, A., Schwartz, M., & Friedman, N. (2013) · Frontiers in Immunology · doi:10.3389/fimmu.2013.00379 · Cited by 37 · see citing works

Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads

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T cell receptor alpha variable 12‐2 bias in the immunodominant response to Yellow fever virus

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Abundant cytomegalovirus (CMV) reactive clonotypes in the CD8+ T cell receptor alpha repertoire following allogeneic transplantation

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Biased IGH VDJ gene repertoire and clonal expansions in B cells of chronically hepatitis C virus–infected individuals

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Direct high‐throughput amplification and sequencing of immunoglobulin genes from single human B cells

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Antigen-Driven Patterns of TCR Bias Are Shared across Diverse Outcomes of Human Hepatitis C Virus Infection

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Highly Accurate Sequencing of Full-Length Immune Repertoire Amplicons Using Tn5-Enabled and Molecular Identifier–Guided Amplicon Assembly

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T-cell receptor-α repertoire of CD8+ T cells following allogeneic stem cell transplantation using next-generation sequencing

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Donor CD4 T Cell Diversity Determines Virus Reactivation in Patients After HLA-Matched Allogeneic Stem Cell Transplantation

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RepSeq Data Representativeness and Robustness Assessment by Shannon Entropy

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Characteristic analysis of TCR β-chain CDR3 repertoire for pre- and post-liver transplantation

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Dynamics of B Cell Recovery In Kidney/Bone Marrow Transplant Recipients

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On the feasibility of mining CD8+ T-cell receptor patterns underlying immunogenic peptide recognitionPreprint

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T cell clonal expansions in ileal Crohn's disease are associated with smoking behaviour and postoperative recurrence

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The technological landscape and applications of single-cell multi-omics

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Adaptive Immunity

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Persisting adaptive immunity to SARS-CoV-2 in Lower AustriaPreprint

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