VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires von Shugay, Mikhail, Bagaev, Dmitriy V, Turchaninova, Maria A, Bolotin, Dmitriy A, Britanova, Olga V, Putintseva, Ekaterina V, Pogorelyy, Mikhail V, Nazarov, Vadim I, Zvyagin, Ivan V, Kirgizova, Vitalina I, Kirgizov, Kirill I, Skorobogatova, Elena V, Chudakov, Dmitriy M

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Autoimmunity-associated T cell receptors recognize HLA-B27-bound peptides von Yang, Xinbo, Garner, Lee I., Zvyagin, Ivan V., Paley, Michael A., Komech, Ekaterina A., Jude, Kevin M., Zhao, Xiang, Fernandes, Ricardo A., Hassman, Lynn M., Paley, Grace L., Savvides, Christina S., Brackenridge, Simon, Quastel, Max N., Chudakov, Dmitriy M., Bowness, Paul, Yokoyama, Wayne M., McMichael, Andrew J., Gillespie, Geraldine M., Garcia, K. Christopher

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Detecting T-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires von Pavlova, Anastasia V, Zvyagin, Ivan V, Shugay, Mikhail

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Next generation sequencing for TCR repertoire profiling: Platform‐specific features and correction algorithms von Bolotin, Dmitry A., Mamedov, Ilgar Z., Britanova, Olga V., Zvyagin, Ivan V., Shagin, Dmitriy, Ustyugova, Svetlana V., Turchaninova, Maria A., Lukyanov, Sergey, Lebedev, Yury B., Chudakov, Dmitriy M.

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Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing von Zvyagin, Ivan V., Pogorelyy, Mikhail V., Ivanova, Marina E., Komech, Ekaterina A., Shugay, Mikhail, Bolotin, Dmitry A., Shelenkov, Andrey A., Kurnosov, Alexey A., Staroverov, Dmitriy B., Chudakov, Dmitriy M., Lebedev, Yuri B., Mamedov, Ilgar Z.

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Large-scale template-based structural modeling of T-cell receptors with known antigen specificity reveals complementarity features von Shcherbinin, Dmitrii S., Karnaukhov, Vadim K., Zvyagin, Ivan V., Chudakov, Dmitriy M., Shugay, Mikhail

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HLA variants have different preferences to present proteins with specific molecular functions which are complemented in frequent haplotypes von Karnaukhov, Vadim, Paes, Wayne, Woodhouse, Isaac B, Partridge, Thomas, Nicastri, Annalisa, Brackenridge, Simon, Shcherbinin, Dmitrii, Chudakov, Dmitry M, Zvyagin, Ivan V, Ternette, Nicola, Koohy, Hashem, Borrow, Persephone, Shugay, Mikhail

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Deconvolution of B cell receptor repertoire in multiple sclerosis patients revealed a delay in tBreg maturation von Lomakin, Yakov A., Zvyagin, Ivan V., Ovchinnikova, Leyla A., Kabilov, Marsel R., Staroverov, Dmitriy B., Mikelov, Artem, Tupikin, Alexey E., Zakharova, Maria Y., Bykova, Nadezda A., Mukhina, Vera S., Favorov, Alexander V., Ivanova, Maria, Simaniv, Taras, Rubtsov, Yury P., Chudakov, Dmitriy M., Zakharova, Maria N., Illarioshkin, Sergey N., Belogurov, Alexey A., Gabibov, Alexander G.

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Inactivated tick-borne encephalitis vaccine elicits several overlapping waves of T cell response von Sycheva, Anastasiia L, Komech, Ekaterina A, Pogorelyy, Mikhail V, Minervina, Anastasia A, Urazbakhtin, Shamil Z, Salnikova, Maria A, Vorovitch, Mikhail F, Kopantzev, Eugene P, Zvyagin, Ivan V, Komkov, Alexander Y, Mamedov, Ilgar Z, Lebedev, Yuri B

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Memory persistence and differentiation into antibody-secreting cells accompanied by positive selection in longitudinal BCR repertoires von Mikelov, Artem, Alekseeva, Evgeniia I, Komech, Ekaterina A, Staroverov, Dmitry B, Turchaninova, Maria A, Shugay, Mikhail, Chudakov, Dmitriy M, Bazykin, Georgii A, Zvyagin, Ivan V

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TCR repertoire profiling revealed antigen-driven CD8+ T cell clonal groups shared in synovial fluid of patients with spondyloarthritis von Komech, Ekaterina A., Koltakova, Anastasia D., Barinova, Anna A., Minervina, Anastasia A., Salnikova, Maria A., Shmidt, Evgeniya I., Korotaeva, Tatiana V., Loginova, Elena Y., Erdes, Shandor F., Bogdanova, Ekaterina A., Shugay, Mikhail, Lukyanov, Sergey, Lebedev, Yury B., Zvyagin, Ivan V.

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Preparing unbiased T-cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling von Mamedov, Ilgar Z, Britanova, Olga V, Zvyagin, Ivan V, Turchaninova, Maria A, Bolotin, Dmitriy A, Putintseva, Ekaterina V, Lebedev, Yuriy B, Chudakov, Dmitriy M

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Clonal structure and the specificity of vaccine-induced T cell response to SARS-CoV-2 Spike protein von Sheetikov, Saveliy A, Khmelevskaya, Alexandra A, Zornikova, Ksenia V, Zvyagin, Ivan V, Shomuradova, Alina S, Serdyuk, Yana V, Shakirova, Naina T, Peshkova, Iuliia O, Titov, Aleksei, Romaniuk, Dmitrii S, Shagina, Irina A, Chudakov, Dmitry M, Kiryukhin, Dmitry O, Shcherbakova, Olga V, Khamaganova, Ekaterina G, Dzutseva, Vitalina, Afanasiev, Andrei, Bogolyubova, Apollinariya V, Efimov, Grigory A

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Exploring the pre-immune landscape of antigen-specific T cells von Pogorelyy, Mikhail V, Fedorova, Alla D, McLaren, James E, Ladell, Kristin, Bagaev, Dmitri V, Eliseev, Alexey V, Mikelov, Artem I, Koneva, Anna E, Zvyagin, Ivan V, Price, David A, Chudakov, Dmitry M, Shugay, Mikhail

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VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium von Bagaev, Dmitry V, Vroomans, Renske M A, Samir, Jerome, Stervbo, Ulrik, Rius, Cristina, Dolton, Garry, Greenshields-Watson, Alexander, Attaf, Meriem, Egorov, Evgeny S, Zvyagin, Ivan V, Babel, Nina, Cole, David K, Godkin, Andrew J, Sewell, Andrew K, Kesmir, Can, Chudakov, Dmitriy M, Luciani, Fabio, Shugay, Mikhail

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Surface NKG2C Identifies Differentiated αβT-Cell Clones Expanded in Peripheral Blood von Kovalenko, Elena I, Zvyagin, Ivan V, Streltsova, Maria A, Mikelov, Artem I, Erokhina, Sofya A, Telford, William G, Sapozhnikov, Alexander M, Lebedev, Yury B

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Clonal diversity predicts persistence of SARS-CoV-2 epitope-specific T-cell response von Zornikova, Ksenia V., Khmelevskaya, Alexandra, Sheetikov, Savely A., Kiryukhin, Dmitry O., Shcherbakova, Olga V., Titov, Aleksei, Zvyagin, Ivan V., Efimov, Grigory A.

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VDJdb: a curated database of T-cell receptor sequences with known antigen specificity von Shugay, Mikhail, Bagaev, Dmitriy V, Zvyagin, Ivan V, Vroomans, Renske M, Crawford, Jeremy Chase, Dolton, Garry, Komech, Ekaterina A, Sycheva, Anastasiya L, Koneva, Anna E, Egorov, Evgeniy S, Eliseev, Alexey V, Van Dyk, Ewald, Dash, Pradyot, Attaf, Meriem, Rius, Cristina, Ladell, Kristin, McLaren, James E, Matthews, Katherine K, Clemens, E Bridie, Douek, Daniel C, Luciani, Fabio, van Baarle, Debbie, Kedzierska, Katherine, Kesmir, Can, Thomas, Paul G, Price, David A, Sewell, Andrew K, Chudakov, Dmitriy M

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tcR: an R package for T cell receptor repertoire advanced data analysis von Nazarov, Vadim I, Pogorelyy, Mikhail V, Komech, Ekaterina A, Zvyagin, Ivan V, Bolotin, Dmitry A, Shugay, Mikhail, Chudakov, Dmitry M, Lebedev, Yury B, Mamedov, Ilgar Z

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MiTCR: software for T-cell receptor sequencing data analysis von Bolotin, Dmitriy A, Shugay, Mikhail, Mamedov, Ilgar Z, Putintseva, Ekaterina V, Turchaninova, Maria A, Zvyagin, Ivan V, Britanova, Olga V, Chudakov, Dmitriy M

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