Towards error-free profiling of immune repertoires

IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis

Brochet, X., Lefranc, M.-P., & Giudicelli, V. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn316 · Cited by 1,216

IgBLAST: an immunoglobulin variable domain sequence analysis tool

Ye, J., Ma, N., Madden, T. L., & Ostell, J. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt382 · Cited by 1,189

Single-cell sequencing-based technologies will revolutionize whole-organism science

Shapiro, E., Biezuner, T., & Linnarsson, S. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3542 · Cited by 1,177

Detection and quantification of rare mutations with massively parallel sequencing

Kinde, I., Wu, J., Papadopoulos, N., Kinzler, K. W., & Vogelstein, B. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1105422108 · Cited by 1,144

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

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

Age-Related Decrease in TCR Repertoire Diversity Measured with Deep and Normalized Sequence Profiling

Britanova, O. V., Putintseva, E. V., Shugay, M., Merzlyak, E. M., Turchaninova, M. A., Staroverov, D. B., Bolotin, D. A., Lukyanov, S., Bogdanova, E. A., Mamedov, I. Z., et al. (2014) · The Journal of Immunology · doi:10.4049/jimmunol.1302064 · Cited by 465

Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire

Glanville, J., Zhai, W., Berka, J., Telman, D., Huerta, G., Mehta, G. R., Ni, I., Mei, L., Sundar, P. D., Day, G. M. R., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909775106 · Cited by 440

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing

Campbell, P. J., Pleasance, E. D., Stephens, P. J., Dicks, E., Rance, R., Goodhead, I., Follows, G. A., Green, A. R., Futreal, P. A., & Stratton, M. R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801523105 · Cited by 365

Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes

Warren, R. L., Freeman, J. D., Zeng, T., Choe, G., Munro, S., Moore, R., Webb, J. R., & Holt, R. A. (2011) · Genome Research · doi:10.1101/gr.115428.110 · Cited by 350

A Novel Approach to the Analysis of Specificity, Clonality, and Frequency of HIV-Specific T Cell Responses Reveals a Potential Mechanism for Control of Viral Escape

Douek, D. C., Betts, M. R., Brenchley, J. M., Hill, B. J., Ambrozak, D. R., Ngai, K.-L., Karandikar, N. J., Casazza, J. P., & Koup, R. A. (2002) · The Journal of Immunology · doi:10.4049/jimmunol.168.6.3099 · Cited by 204

Effects of Aging, Cytomegalovirus Infection, and EBV Infection on Human B Cell Repertoires

Wang, C., Liu, Y., Xu, L. T., Jackson, K. J. L., Roskin, K. M., Pham, T. D., Laserson, J., Marshall, E. L., Seo, K., Lee, J.-Y., et al. (2014) · The Journal of Immunology · doi:10.4049/jimmunol.1301384 · Cited by 183

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., 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 178

MiTCR: software for T-cell receptor sequencing data analysis

Bolotin, D. A., Shugay, M., Mamedov, I. Z., Putintseva, E. V., Turchaninova, M. A., Zvyagin, I. V., Britanova, O. V., & Chudakov, D. M. (2013) · Nature Methods · doi:10.1038/nmeth.2555 · Cited by 173

High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment

Logan, A. C., Gao, H., Wang, C., Sahaf, B., Jones, C. D., Marshall, E. L., Buño, I., Armstrong, R., Fire, A. Z., Weinberg, K. I., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1118357109 · Cited by 167

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

Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populationsPreprint

Bashford-Rogers, R. J. M., Palser, A. L., Huntly, B. J. P., Rance, R., Vassiliou, G. S., Follows, G., & Kellam, P. (2013) · Genome Research · doi:10.1101/gr.154815.113 · Cited by 142

Deep Sequencing of Antiviral T-Cell Responses to HCMV and EBV in Humans Reveals a Stable Repertoire That Is Maintained for Many Years

Klarenbeek, P. L., Remmerswaal, E. B. M., ten Berge, I. J. M., Doorenspleet, M. E., van Schaik, B. D. C., Esveldt, R. E., Koch, S. D., ten Brinke, A., van Kampen, A. H. C., Bemelman, F. J., et al. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1002889 · Cited by 110

PCR-Induced Transitions Are the Major Source of Error in Cleaned Ultra-Deep Pyrosequencing Data

Brodin, J., Mild, M., Hedskog, C., Sherwood, E., Leitner, T., Andersson, B., & Albert, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0070388 · Cited by 75

Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire

Nguyen, P., Ma, J., Pei, D., Obert, C. A., Cheng, C., & Geiger, T. L. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-106 · Cited by 73

Quantitative tracking of T cell clones after haematopoietic stem cell transplantation

Mamedov, I. Z., Britanova, O. V., Bolotin, D. A., Chkalina, A. V., Staroverov, D. B., Zvyagin, I. V., Kotlobay, A. A., Turchaninova, M. A., Анатольевич, Ф. Д., Novik, A. A., et al. (2011) · EMBO Molecular Medicine · doi:10.1002/emmm.201100129 · Cited by 64

Mother and Child T Cell Receptor Repertoires: Deep Profiling Study

Putintseva, E. V., Britanova, O. V., Staroverov, D. B., Merzlyak, E. M., Turchaninova, M. A., Shugay, M., Bolotin, D. A., Pogorelyy, M. V., Mamedov, I. Z., Bobrynina, V. O., et al. (2013) · Frontiers in Immunology · doi:10.3389/fimmu.2013.00463 · Cited by 45

First autologous hematopoietic SCT for ankylosing spondylitis: a case report and clues to understanding the therapy

Britanova, O. V., Bochkova, A. G., Staroverov, D. B., Анатольевич, Ф. Д., Bolotin, D. A., Mamedov, I. Z., Turchaninova, M. A., Putintseva, E. V., Kotlobay, A. A., Lukyanov, S., et al. (2012) · Bone Marrow Transplantation · doi:10.1038/bmt.2012.44 · Cited by 26

A Multifunctional AAV-CRISPR-Cas9 and Its Host Response

Chew, W. L., Tabebordbar, M., Cheng, J. K. W., Mali, P., Wu, E. Y., Ng, A. H. M., Zhu, K., Wagers, A. J., & Church, G. M. (2016) · Nature Methods · doi:10.1038/nmeth.3993 · Cited by 617

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. I., et al. (2015) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004503 · Cited by 614

T cell fate and clonality inference from single-cell transcriptomes

(2016) · doi:10.1038/nmeth.3800 · Cited by 434

Two subsets of stem-like CD8+ memory T cell progenitors with distinct fate commitments in humans

Galletti, G., De Simone, G., Mazza, E. M. C., Puccio, S., Mezzanotte, C., Bi, T. M., Davydov, A. N., Metsger, M., Scamardella, E., Alvisi, G., et al. (2020) · Nature Immunology · doi:10.1038/s41590-020-0791-5 · Cited by 299

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