MiXCR: software for comprehensive adaptive immunity profiling
Bolotin, Dmitriy A, Poslavsky, Stanislav, Mitrophanov, Igor, Shugay, Mikhail, Mamedov, Ilgar Z, Putintseva, Ekaterina V, Chudakov, Dmitriy M
Published in Nature methods (01.05.2015)
Published in Nature methods (01.05.2015)
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Journal Article
Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer
Plitas, George, Konopacki, Catherine, Wu, Kenmin, Bos, Paula D., Morrow, Monica, Putintseva, Ekaterina V., Chudakov, Dmitriy M., Rudensky, Alexander Y.
Published in Immunity (Cambridge, Mass.) (15.11.2016)
Published in Immunity (Cambridge, Mass.) (15.11.2016)
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Clonal selection in the human Vδ1 T cell repertoire indicates γδ TCR-dependent adaptive immune surveillance
Davey, Martin S., Willcox, Carrie R., Joyce, Stephen P., Ladell, Kristin, Kasatskaya, Sofya A., McLaren, James E., Hunter, Stuart, Salim, Mahboob, Mohammed, Fiyaz, Price, David A., Chudakov, Dmitriy M., Willcox, Benjamin E.
Published in Nature communications (01.03.2017)
Published in Nature communications (01.03.2017)
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VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires
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
Published in PLoS computational biology (01.11.2015)
Published in PLoS computational biology (01.11.2015)
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Towards error-free profiling of immune repertoires
Shugay, Mikhail, Britanova, Olga V, Merzlyak, Ekaterina M, Turchaninova, Maria A, Mamedov, Ilgar Z, Tuganbaev, Timur R, Bolotin, Dmitriy A, Staroverov, Dmitry B, Putintseva, Ekaterina V, Plevova, Karla, Linnemann, Carsten, Shagin, Dmitriy, Pospisilova, Sarka, Lukyanov, Sergey, Schumacher, Ton N, Chudakov, Dmitriy M
Published in Nature methods (01.06.2014)
Published in Nature methods (01.06.2014)
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Journal Article
The human Vδ2+ T-cell compartment comprises distinct innate-like Vγ9+ and adaptive Vγ9- subsets
Davey, Martin S., Willcox, Carrie R., Hunter, Stuart, Kasatskaya, Sofya A., Remmerswaal, Ester B. M., Salim, Mahboob, Mohammed, Fiyaz, Bemelman, Frederike J., Chudakov, Dmitriy M., Oo, Ye H., Willcox, Benjamin E.
Published in Nature communications (02.05.2018)
Published in Nature communications (02.05.2018)
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Far-red fluorescent tags for protein imaging in living tissues
Shcherbo, Dmitry, Murphy, Christopher S, Ermakova, Galina V, Solovieva, Elena A, Chepurnykh, Tatiana V, Shcheglov, Aleksandr S, Verkhusha, Vladislav V, Pletnev, Vladimir Z, Hazelwood, Kristin L, Roche, Patrick M, Lukyanov, Sergey, Zaraisky, Andrey G, Davidson, Michael W, Chudakov, Dmitriy M
Published in Biochemical journal (15.03.2009)
Published in Biochemical journal (15.03.2009)
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Journal Article
Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection
Minervina, Anastasia A, Komech, Ekaterina A, Titov, Aleksei, Bensouda Koraichi, Meriem, Rosati, Elisa, Mamedov, Ilgar Z, Franke, Andre, Efimov, Grigory A, Chudakov, Dmitriy M, Mora, Thierry, Walczak, Aleksandra M, Lebedev, Yuri B, Pogorelyy, Mikhail V
Published in eLife (05.01.2021)
Published in eLife (05.01.2021)
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CD4+ T Follicular Helper Cells in Human Tonsils and Blood Are Clonally Convergent but Divergent from Non-Tfh CD4+ Cells
Brenna, Elena, Davydov, Alexey N., Ladell, Kristin, McLaren, James E., Bonaiuti, Paolo, Metsger, Maria, Ramsden, James D., Gilbert, Sarah C., Lambe, Teresa, Price, David A., Campion, Suzanne L., Chudakov, Dmitriy M., Borrow, Persephone, McMichael, Andrew J.
Published in Cell reports (Cambridge) (07.01.2020)
Published in Cell reports (Cambridge) (07.01.2020)
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Journal Article
Tracking intracellular protein movements using photoswitchable fluorescent proteins PS-CFP2 and Dendra2
Lukyanov, Konstantin A, Chudakov, Dmitriy M, Lukyanov, Sergey
Published in Nature protocols (01.08.2007)
Published in Nature protocols (01.08.2007)
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HRES-1/Rab4-mediated depletion of Drp1 impairs mitochondrial homeostasis and represents a target for treatment in SLE
Caza, Tiffany N, Fernandez, David R, Talaber, Gergely, Oaks, Zachary, Haas, Mark, Madaio, Michael P, Lai, Zhi-wei, Miklossy, Gabriella, Singh, Ram R, Chudakov, Dmitriy M, Malorni, Walter, Middleton, Frank, Banki, Katalin, Perl, Andras
Published in Annals of the rheumatic diseases (01.10.2014)
Published in Annals of the rheumatic diseases (01.10.2014)
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Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires
Pogorelyy, Mikhail V, Elhanati, Yuval, Marcou, Quentin, Sycheva, Anastasiia L, Komech, Ekaterina A, Nazarov, Vadim I, Britanova, Olga V, Chudakov, Dmitriy M, Mamedov, Ilgar Z, Lebedev, Yury B, Mora, Thierry, Walczak, Aleksandra M
Published in PLoS computational biology (01.07.2017)
Published in PLoS computational biology (01.07.2017)
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Deep cfDNA fragment end profiling enables cancer detection
Zhitnyuk, Yulia V, Koval, Anastasia P, Alferov, Aleksandr A, Shtykova, Yanina A, Mamedov, Ilgar Z, Kushlinskii, Nikolay E, Chudakov, Dmitriy M, Shcherbo, Dmitry S
Published in Molecular cancer (21.01.2022)
Published in Molecular cancer (21.01.2022)
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SARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19
Stanevich, Oksana V., Alekseeva, Evgeniia I., Sergeeva, Maria, Fadeev, Artem V., Komissarova, Kseniya S., Ivanova, Anna A., Simakova, Tamara S., Vasilyev, Kirill A., Shurygina, Anna-Polina, Stukova, Marina A., Safina, Ksenia R., Nabieva, Elena R., Garushyants, Sofya K., Klink, Galya V., Bakin, Evgeny A., Zabutova, Jullia V., Kholodnaia, Anastasia N., Lukina, Olga V., Skorokhod, Irina A., Ryabchikova, Viktoria V., Medvedeva, Nadezhda V., Lioznov, Dmitry A., Danilenko, Daria M., Chudakov, Dmitriy M., Komissarov, Andrey B., Bazykin, Georgii A.
Published in Nature communications (10.01.2023)
Published in Nature communications (10.01.2023)
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Next generation sequencing for TCR repertoire profiling: Platform‐specific features and correction algorithms
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.
Published in European journal of immunology (01.11.2012)
Published in European journal of immunology (01.11.2012)
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Bright far-red fluorescent protein for whole-body imaging
Chudakov, Dmitriy M, Shcherbo, Dmitry, Merzlyak, Ekaterina M, Chepurnykh, Tatiana V, Fradkov, Arkady F, Ermakova, Galina V, Solovieva, Elena A, Lukyanov, Konstantin A, Bogdanova, Ekaterina A, Zaraisky, Andrey G, Lukyanov, Sergey
Published in Nature methods (01.09.2007)
Published in Nature methods (01.09.2007)
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The Changing Landscape of Naive T Cell Receptor Repertoire With Human Aging
Egorov, Evgeny S, Kasatskaya, Sofya A, Zubov, Vasiliy N, Izraelson, Mark, Nakonechnaya, Tatiana O, Staroverov, Dmitriy B, Angius, Andrea, Cucca, Francesco, Mamedov, Ilgar Z, Rosati, Elisa, Franke, Andre, Shugay, Mikhail, Pogorelyy, Mikhail V, Chudakov, Dmitriy M, Britanova, Olga V
Published in Frontiers in immunology (24.07.2018)
Published in Frontiers in immunology (24.07.2018)
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Large-scale template-based structural modeling of T-cell receptors with known antigen specificity reveals complementarity features
Shcherbinin, Dmitrii S., Karnaukhov, Vadim K., Zvyagin, Ivan V., Chudakov, Dmitriy M., Shugay, Mikhail
Published in Frontiers in immunology (15.08.2023)
Published in Frontiers in immunology (15.08.2023)
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Journal Article
Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones
Minervina, Anastasia A, Pogorelyy, Mikhail V, Komech, Ekaterina A, Karnaukhov, Vadim K, Bacher, Petra, Rosati, Elisa, Franke, Andre, Chudakov, Dmitriy M, Mamedov, Ilgar Z, Lebedev, Yuri B, Mora, Thierry, Walczak, Aleksandra M
Published in eLife (21.02.2020)
Published in eLife (21.02.2020)
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