Dmitriy Chudakov, Ph.D.

2019

• Li, N; van Unen, V; Abdelaal, T; Guo, NN; Kasatskaya, SA; Ladell, K; McLaren, JE; Egorov, ES; Izraelson, M; Lopes, SMCD; Hollt, T; Britanova, OV; Eggermont, J; de Miranda, NFCC; Chudakov, DM; Price, DA; Lelieveldt, BPF; Koning, F, 2019: Memory CD4(+) T cells are generated in the human fetal intestine. NATURE IMMUNOLOGY 20(3), p. 301 - +, doi: 10.1038/s41590-018-0294-9
• Siewert, K; Molin, S; Bacher, P; Scheffold, A; Kuhl, H; Timmermann, B; Chudakov, D; Thierse, HJ; Luch, A, 2019: Skin enrichment of nickel-activated CD154+CD4+memory T cells in acute allergic contact dermatitis. NAUNYN-SCHMIEDEBERGS ARCHIVES OF PHARMACOLOGY 392, p. S65 - S65
• Pogorelyy, MV; Minervina, AA; Shugay, M; Chudakov, DM; Lebedev, YB; Mora, T; Walczak, AM, 2019: Detecting T cell receptors involved in immune responses from single repertoire snapshots. PLOS BIOLOGY 17(6), doi: 10.1371/journal.pbio.3000314
• Weber, J; de la Rosa, J; Grove, CS; Schick, M; Rad, L; Baranovt, O; Strong, A; Pfaus, A; Friedrich, MJ; Engleitner, T; Lersch, R; Ollinger, R; Grau, M; Menendez, IG; Martella, M; Kohlhofer, U; Banerjee, R; Turchaninova, MA; Scherger, A; Hoffman, GJ; Hess, J; Kuh, LB; Ammon, T; Kim, J; Schneider, G; Unger, K; Zimber-Strobl, U; Heikenwalder, M; Schmidt-Supprian, M; Yang, FT; Saur, D; Liu, PT; Steiger, K; Chudakov, DM; Lenz, G; Quintanilla-Martinez, L; Keller, U; Vassiliou, GS; Cadinanos, J; Bradley, A; Rad, R, 2019: PiggyBac transposon tools for recessive screening identify B-cell lymphoma drivers in mice. NATURE COMMUNICATIONS 10, doi: 10.1038/s41467-019-09180-3

2018

• Sycheva, AL; Pogorelyy, MV; Komech, EA; Minervina, AA; Zvyagin, IV; Staroverov, DB; Chudakov, DM; Lebedev, YB; Mamedov, IZ, 2018: Quantitative profiling reveals minor changes of T cell receptor repertoire in response to subunit inactivated influenza vaccine. VACCINE 36(12), p. 1599 - 1605, doi: 10.1016/j.vaccine.2018.02.027
• Davey, MS; Willcox, CR; Hunter, S; Kasatskaya, SA; Remmerswaal, EBM; Salim, M; Mohammed, F; Bemelman, FJ; Chudakov, DM; Oo, YH; Willcox, BE, 2018: The human V delta 2(+) T-cell compartment comprises distinct innate-like V gamma 9(+) and adaptive V gamma 9(-) subsets. NATURE COMMUNICATIONS 9, doi: 10.1038/s41467-018-04076-0
• Pogorelyy, MV; Fedorova, AD; McLaren, JE; Ladell, K; Bagaev, DV; Eliseev, AV; Mikelov, AI; Koneva, AE; Zvyagin, IV; Price, DA; Chudakov, DM; Shugay, M, 2018: Exploring the pre-immune landscape of antigen-specific T cells. GENOME MEDICINE 10, doi: 10.1186/s13073-018-0577-7
• Hunter, S; Willcox, CR; Davey, MS; Kasatskaya, SA; Jeffery, HC; Chudakov, DM; Oo, YH; Willcox, BE, 2018: Human liver infiltrating gamma delta T cells are composed of clonally expanded circulating and tissue-resident populations. JOURNAL OF HEPATOLOGY 69(3), p. 654 - 665, doi: 10.1016/j.jhep.2018.05.007
• Fan, XY; Moltedo, B; Mendoza, A; Dayydov, AN; Faire, MB; Mazutis, L; Sharma, R; Pe´er, D; Chudakov, DM; Rudensky, AY, 2018: CD49b defines functionally mature Treg cells that survey skin and vascular tissues. JOURNAL OF EXPERIMENTAL MEDICINE 215(11), p. 2796 - 2814, doi: 10.1084/jem.20181442
• Bolotin, DA; Poslavsky, S; Davydov, AN; Chudakov, DM, 2018: Evaluation of immune repertoire inference methods from RNA-seq data reply. NATURE BIOTECHNOLOGY 36(11), p. 1035 - 1036, doi: 10.1038/nbt.4296
• Pogorelyy, MV; Minervina, AA; Touzel, MP; Sycheva, AL; Komech, EA; Kovalenko, EI; Karganova, GG; Egorov, ES; Komkov, AY; Chudakov, DM; Mamedov, IZ; Mora, T; Walczak, AM; Lebedev, YB, 2018: Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 115(50), p. 12704 - 12709, doi: 10.1073/pnas.1809642115
• Pogorelyy, MV; Minervina, AA; Chudakov, DM; Mamedov, IZ; Lebedev, YB; Mora, T; Walczak, AM, 2018: Method for identification of condition associated public antigen receptor sequences. ELIFE 7, doi: 10.7554/elife.33050
• Komech, EA; Pogorelyy, MV; Egorov, ES; Britanova, OV; Rebrikov, DV; Bochkova, AG; Shmidt, EI; Shostak, NA; Shugay, M; Lukyanov, S; Mamedov, IZ; Lebedev, YB; Chudakov, DM; Zvyagin, IV, 2018: CD8(+) T cells with characteristic T cell receptor beta motif are detected in blood and expanded in synovial fluid of ankylosing spondylitis patients. RHEUMATOLOGY 57(6), p. 1097 - 1104, doi: 10.1093/rheumatology/kex517
• Izraelson, M; Nakonechnaya, TO; Moltedo, B; Egorov, ES; Kasatskaya, SA; Putintseva, EV; Mamedov, IZ; Staroverov, DB; Shemiakina, II; Zakharova, MY; Davydov, AN; Bolotin, DA; Shugay, M; Chudakov, DM; Rudensky, AY; Britanova, OV, 2018: Comparative analysis of murine T-cell receptor repertoires. IMMUNOLOGY 153(2), p. 133 - 144, doi: 10.1111/imm.12857
• Shugay, M; Bagaev, DV; Zvyagin, IV; Vroomans, RM; Crawford, JC; Dolton, G; Komech, EA; Sycheva, AL; Koneva, AE; Egorov, ES; Eliseev, AV; Van Dyk, E; Dash, P; Attaf, M; Rius, C; Ladell, K; McLaren, JE; Matthews, KK; Clemens, EB; Douek, DC; Luciani, F; van Baarle, D; Kedzierska, K; Kesmir, C; Thomas, PG; Price, DA; Sewell, AK; Chudakov, DM, 2018: VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. NUCLEIC ACIDS RESEARCH 46(D1), p. D419 - D427, doi: 10.1093/nar/gkx760

2017

• Zvyagin, IV; Mamedov, IZ; Tatarinova, OV; Komech, EA; Kurnikova, EE; Boyakova, EV; Brilliantova, V; Shelikhova, LN; Balashov, DN; Shugay, M; Sycheva, AL; Kasatskaya, SA; Lebedev, YB; Maschan, AA; Maschan, MA; Chudakov, DM, 2017: Tracking T-cell immune reconstitution after TCR alpha beta/CD19-depleted hematopoietic cells transplantation in children. LEUKEMIA 31(5), p. 1145 - 1153, doi: 10.1038/leu.2016.321
• Shagin, DA; Turchaninova, MA; Shagina, IA; Shugay, M; Zaretsky, AR; Zueva, OI; Bolotin, DA; Lukyanov, S; Chudakov, DM, 2017: Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries. BMC GENOMICS 18, doi: 10.1186/s12864-017-3815-2
• Shugay, M; Zaretsky, AR; Shagin, DA; Shagina, IA; Volchenkov, IA; Shelenkov, AA; Lebedin, MY; Bagaev, DV; Lukyanov, S; Chudakov, DM, 2017: MAGERI: Computational pipeline for molecular-barcoded targeted resequencing. PLOS COMPUTATIONAL BIOLOGY 13(5), doi: 10.1371/journal.pcbi.1005480
• Levine, AG; Medoza, A; Hemmers, S; Moltedo, B; Niec, RE; Schizas, M; Hoyos, BE; Putintseva, EV; Chaudhry, A; Dikiy, S; Fujisawa, S; Chudakov, DM; Treuting, PM; Rudensky, AY, 2017: Stability and function of regulatory T cells expressing the transcription factor T-bet. NATURE 546(7658), p. 421 - +, doi: 10.1038/nature22360
• Turchaninova, M; Shugay, M; Lebedin, M; Obraztsova, A; Davydov, A; Chudakov, D, 2017: Analysis of immunoglobulin repertoires with unique molecular identifiers. FEBS JOURNAL 284, p. 238 - 238
• Bolotin, DA; Poslavsky, S; Davydov, AN; Frenkel, FE; Fanchi, L; Zolotareva, OI; Hemmers, S; Putintseva, EV; Obraztsova, AS; Shugay, M; Ataullakhanov, RI; Rudensky, AY; Schumacher, TN; Chudakov, DM, 2017: Antigen receptor repertoire profiling from RNA-seq data. NATURE BIOTECHNOLOGY 35(10), p. 908 - 911, doi: 10.1038/nbt.3979
• Kost, LA; Nikitin, ES; Ivanova, VO; Sung, U; Putintseva, EV; Chudakov, DM; Balaban, PM; Lukyanov, KA; Bogdanov, AM, 2017: Insertion of the voltage-sensitive domain into circularly permuted red fluorescent protein as a design for genetically encoded voltage sensor. PLOS ONE 12(9), doi: 10.1371/journal.pone.0184225
• Egorov, E; Kasatskaya, S; Izraelson, M; Nakonechnaya, T; Chudakov, D; Britanova, O, 2017: Landscapes of t cell receptor repertoires. FEBS JOURNAL 284, p. 239 - 240
• Pogorelyy, MV; Elhanati, Y; Marcou, Q; Sycheva, AL; Komech, EA; Nazarov, VI; Britanova, OV; Chudakov, DM; Mamedov, IZ; Lebedev, YB; Mora, T; Walczak, AM, 2017: Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires. PLOS COMPUTATIONAL BIOLOGY 13(7), doi: 10.1371/journal.pcbi.1005572
• Davey, M S; Willcox, C R; Joyce, S P; Ladell, K; Kasatskaya, S A; McLaren, J E; Hunter, S; Salim, M; Mohammed, F; Price, D A; Chudakov, D M; Willcox, B E, 2017: Clonal selection in the human V delta 1 T cell repertoire indicates gamma delta TCR-dependent adaptive immune surveillance.. NATURE COMMUNICATIONS , doi: 10.1038/ncomms14760
• Shagin, DA; Shagina, IA; Zaretsky, AR; Barsova, EV; Kelmanson, IV; Lukyanov, S; Chudakov, DM; Shugay, M, 2017: A high-throughput assay for quantitative measurement of PCR errors. SCIENTIFIC REPORTS 7, doi: 10.1038/s41598-017-02727-8
• Davey, MS; Willcox, CR; Joyce, SP; Ladell, K; Kasatskaya, SA; McLaren, JE; Hunter, S; Salim, M; Mohammed, F; Price, DA; Chudakov, DM; Willcox, BE, 2017: Clonal selection in the human V delta 1 T cell repertoire indicates gamma delta TCR-dependent adaptive immune surveillance. NATURE COMMUNICATIONS 8, doi: 10.1038/ncomms14760

2016

• Sarkisyan, KS; Bolotin, DA; Meer, MV; Usmanova, DR; Mishin, AS; Sharonov, GV; Ivankov, DN; Bozhanova, NG; Baranov, MS; Soylemez, O; Bogatyreva, NS; Vlasov, PK; Egorov, ES; Logacheva, MD; Kondrashov, AS; Chudakov, DM; Putintseva, EV; Mamedov, IZ; Tawfik, DS; Lukyanov, KA; Kondrashov, FA, 2016: Local fitness landscape of the green fluorescent protein. NATURE 533(7603), p. 397 - 401, doi: 10.1038/nature17995
• Britanova, OV; Shugay, M; Merzlyak, EM; Staroverov, DB; Putintseva, EV; Turchaninova, MA; Mamedov, IZ; Pogorelyy, MV; Bolotin, DA; Izraelson, M; Davydov, AN; Egorov, ES; Kasatskaya, SA; Rebrikov, DV; Lukyanov, S; Chudakov, DM, 2016: Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians. JOURNAL OF IMMUNOLOGY 196(12), p. 5005 - 5013, doi: 10.4049/jimmunol.1600005
• Turchaninova, MA; Davydov, A; Britanova, OV; Shugay, M; Bikos, V; Egorov, ES; Kirgizova, VI; Merzlyak, EM; Staroverov, DB; Bolotin, DA; Mamedov, IZ; Izraelson, M; Logacheva, MD; Kladova, O; Plevova, K; Pospisilova, S; Chudakov, DM, 2016: High-quality full-length immunoglobulin profiling with unique molecular barcoding. NATURE PROTOCOLS 11(9), p. 1599 - 1616, doi: 10.1038/nprot.2016.093
• Plitas, G; Konopacki, C; Wu, KM; Bos, PD; Morrow, M; Putintseva, EV; Chudakov, DM; Rudensky, AY, 2016: Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer. IMMUNITY 45(5), p. 1122 - 1134, doi: 10.1016/j.immuni.2016.10.032
• Bagaev, DV; Zvyagin, IV; Putintseva, EV; Izraelson, M; Britanova, OV; Chudakov, DM; Shugay, M, 2016: VDJviz: a versatile browser for immunogenomics data. BMC GENOMICS 17, doi: 10.1186/s12864-016-2799-7
• Britanova, OV; Shugay, M; Merzlyak, EM; Staroverov, DB; Putintseva, EV; Turchaninova, MA; Mamedov, IZ; Pogorelyy, MV; Bolotin, DA; Izraelson, M; Davydov, AN; Egorov, ES; Kasatskaya, SA; Rebrikov, DV; Lukyanov, S; Chudakov, DM, 2016: Long-term dynamics of individual T-cell receptor beta repertoires. EUROPEAN JOURNAL OF IMMUNOLOGY 46, p. 880 - 881
• Pogorelyy, M; Elhanati, Y; Marcou, Q; Sycheva, A; Komech, E; Britanova, O; Chudakov, D; Mamedov, I; Lebedev, Y; Mora, T; Walczak, A, 2016: Persisting fetal clonotypes influence the structure and overlap of adult human TCR repertoires. EUROPEAN JOURNAL OF IMMUNOLOGY 46, p. 52 - 52
• Nazarov, VI; Minervina, AA; Komkov, AY; Pogorelyy, MV; Maschan, MA; Olshanskaya, YV; Zvyagin, IV; Chudakov, DM; Lebedev, YB; Mamedov, IZ, 2016: Reliability of immune receptor rearrangements as genetic markers for minimal residual disease monitoring. BONE MARROW TRANSPLANTATION 51(10), p. 1408 - 1410, doi: 10.1038/bmt.2016.148
• Joachims, ML; Leehan, KM; Lawrence, C; Pelikan, RC; Moore, JS; Pan, ZJ; Rasmussen, A; Radfar, L; Lewis, DM; Grundahl, KM; Kelly, JA; Wiley, GB; Shugay, M; Chudakov, DM; Lessard, CJ; Stone, DU; Scofield, RH; Montgomery, CG; Sivils, KL; Thompson, LF; Farris, AD, 2016: Single-cell analysis of glandular T cell receptors in Sjogren´s syndrome. JCI INSIGHT 1(8), doi: 10.1172/jci.insight.85609

2015

• Nazarov, VI; Pogorelyy, MV; Komech, EA; Zvyagin, IV; Bolotin, DA; Shugay, M; Chudakov, DM; Lebedev, YB; Mamedov, IZ, 2015: tcR: an R package for T cell receptor repertoire advanced data analysis. BMC BIOINFORMATICS 16, doi: 10.1186/s12859-015-0613-1
• Egorov, ES; Merzlyak, EM; Shelenkov, AA; Britanova, OV; Sharonov, GV; Staroverov, DB; Bolotin, DA; Davydov, AN; Barsova, E; Lebedev, YB; Shugay, M; Chudakov, DM, 2015: Quantitative Profiling of Immune Repertoires for Minor Lymphocyte Counts Using Unique Molecular Identifiers. JOURNAL OF IMMUNOLOGY 194(12), p. 6155 - 6163, doi: 10.4049/jimmunol.1500215
• Luker, KE; Pata, P; Shemiakina, II; Pereverzeva, A; Stacer, AC; Shcherbo, DS; Pletnev, VZ; Skolnaja, M; Lukyanov, KA; Luker, GD; Pata, I; Chudakov, DM, 2015: Comparative study reveals better far-red fluorescent protein for whole body imaging. SCIENTIFIC REPORTS 5, doi: 10.1038/srep10332
• Bolotin, DA; Poslavsky, S; Mitrophanov, I; Shugay, M; Mamedov, IZ; Putintseva, EV; Chudakov, DM, 2015: MiXCR: software for comprehensive adaptive immunity profiling. NATURE METHODS 12(5), p. 380 - 381, doi: 10.1038/nmeth.3364
• Feng, YQ; van der Veeken, J; Shugay, M; Putintseva, EV; Osmanbeyoglu, HU; Dikiy, S; Hoyos, BE; Moltedo, B; Hemmers, S; Treuting, P; Leslie, CS; Chudakov, DM; Rudensky, AY, 2015: A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance. NATURE 528(7580), p. 132 - 136, doi: 10.1038/nature16141
• Shugay, M; Lukyanov, S; Chudakov, DM, 2015: Sequencing rare T-cell populations. ONCOTARGET 6(37), p. 39393 - 39394
• Shugay, M; Bagaev, DV; Turchaninova, MA; Bolotin, DA; Britanova, OV; Putintseva, EV; Pogorelyy, MV; Nazarov, VI; Zvyagin, IV; Kirgizova, VI; Kirgizov, KI; Skorobogatova, EV; Chudakov, DM, 2015: VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLOS COMPUTATIONAL BIOLOGY 11(11), doi: 10.1371/journal.pcbi.1004503

2014

• Caza, TN; Fernandez, DR; Talaber, G; Oaks, Z; Haas, M; Madaio, MP; Lai, ZW; Miklossy, G; Singh, RR; Chudakov, DM; Malorni, W; Middleton, F; Banki, K; Perl, A, 2014: HRES-1/Rab4-mediated depletion of Drp1 impairs mitochondrial homeostasis and represents a target for treatment in SLE. ANNALS OF THE RHEUMATIC DISEASES 73(10), p. 1888 - 1897, doi: 10.1136/annrheumdis-2013-203794
• Britanova, OV; Putintseva, EV; Shugay, M; Merzlyak, EM; Turchaninova, MA; Staroverov, DB; Bolotin, DA; Lukyanov, S; Bogdanova, EA; Mamedov, IZ; Lebedev, YB; Chudakov, DM, 2014: Age-Related Decrease in TCR Repertoire Diversity Measured with Deep and Normalized Sequence Profiling. JOURNAL OF IMMUNOLOGY 192(6), p. 2689 - 2698, doi: 10.4049/jimmunol.1302064
• Shugay, M; Britanova, OV; Merzlyak, EM; Turchaninova, MA; Mamedov, IZ; Tuganbaev, TR; Bolotin, DA; Staroverov, DB; Putintseva, EV; Plevova, K; Linnemann, C; Shagin, D; Pospisilova, S; Lukyanov, S; Schumacher, TN; Chudakov, DM, 2014: Towards error-free profiling of immune repertoires. NATURE METHODS 11(6), p. 653 - +, doi: 10.1038/NMETH.2960
• Zvyagin, IV; Pogorelyy, MV; Ivanova, ME; Komech, EA; Shugay, M; Bolotin, DA; Shelenkov, AA; Kurnosov, AA; Staroverov, DB; Chudakov, DM; Lebedev, YB; Mamedov, IZ, 2014: Distinctive properties of identical twins´ TCR repertoires revealed by high-throughput sequencing. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111(16), p. 5980 - 5985, doi: 10.1073/pnas.1319389111

2013

• EV Putintseva, OV Britanova, DB Staroverov, EM Merzlyak, MA Turchaninov, M Shugay, DA Bolotin, MV Pogorelyy, IZ Mamedov, V Bobrynina, M Maschan, YB Lebedev, DM Chudakov., 2013: Mother and child T cell receptor repertoires: deep profiling study. FRONTIERS IN IMMUNOLOGY 4
• Pletnev, VZ; Pletneva, NV; Lukyanov, KA; Souslova, EA; Fradkov, AF; Chudakov, DM; Chepurnykh, T; Yampolsky, IV; Wlodawer, A; Dauter, Z; Pletnev, S, 2013: Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 69, p. 1850 - 1860, doi: 10.1107/S0907444913015424
• Pletneva, NV; Pletnev, VZ; Souslova, E; Chudakov, DM; Lukyanov, S; Martynov, VI; Arhipova, S; Artemyev, I; Wlodawer, A; Dauter, Z; Pletnev, S, 2013: Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 69, p. 1005 - 1012, doi: 10.1107/S0907444913004034
• Mamedov, IZ; Britanova, OV; Zvyagin, IV; Turchaninova, MA; Bolotin, DA; Putintseva, EV; Lebedev, YB; Chudakov, DM, 2013: Preparing unbiased T-cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling. FRONTIERS IN IMMUNOLOGY 4, doi: 10.3389/fimmu.2013.00456
• Mamedov IZ, Britanova OV, Zvyagin IV, Turchaninova MA, Bolotin DA, Putintseva EV, Lebedev YB, Chudakov DM., 2013: Preparing unbiased T cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling. FRONTIERS IN IMMUNOLOGY
• Shugay, M; Bolotin, DA; Putintseva, EV; Pogorelyy, MV; Mamedov, IZ; Chudakov, DM, 2013: Huge overlap of individual TCR beta repertoires. FRONTIERS IN IMMUNOLOGY 4(4), doi: 10.3389/fimmu.2013.00466
• Turchaninova, MA; Britanova, OV; Bolotin, DA; Shugay, M; Putintseva, EV; Staroverov, DB; Sharonov, G; Shcherbo, D; Zvyagin, IV; Mamedov, IZ; Linnemann, C; Schumacher, TN; Chudakov, DM, 2013: Pairing of T-cell receptor chains via emulsion PCR. EUROPEAN JOURNAL OF IMMUNOLOGY 43(9), p. 2507 - 2515, doi: 10.1002/eji.201343453
• Linnemann, C; Heemskerk, B; Kvistborg, P; Kluin, RJC; Bolotin, DA; Chen, XJ; Bresser, K; Nieuwland, M; Schotte, R; Michels, S; Gomez-Eerland, R; Jahn, L; Hombrink, P; Legrand, N; Shu, CJ; Mamedov, IZ; Velds, A; Blank, CU; Haanen, JBAG; Turchaninova, MA; K, 2013: High-throughput identification of antigen-specific TCRs by TCR gene capture. NATURE MEDICINE 19(11), p. 1534 - +, doi: 10.1038/nm.3359
• Bolotin, DA; Shugay, M; Mamedov, IZ; Putintseva, EV; Turchaninova, MA; Zvyagin, IV; Britanova, OV; Chudakov, DM, 2013: MiTCR: software for T-cell receptor sequencing data analysis. NATURE METHODS 10(9), p. 813 - 814, doi: 10.1038/NMETH.2555

2012

• Shemiakina, II; Ermakova, GV; Cranfill, PJ; Baird, MA; Evans, RA; Souslova, EA; Staroverov, DB; Gorokhovatsky, AY; Putintseva, EV; Gorodnicheva, TV; Chepurnykh, TV; Strukova, L; Lukyanov, S; Zaraisky, AG; Davidson, MW; Chudakov, DM; Shcherbo, D, 2012: A monomeric red fluorescent protein with low cytotoxicity. NATURE COMMUNICATIONS 3, doi: 10.1038/ncomms2208
• Britanova, OV; Bochkova, AG; Staroverov, DB; Fedorenko, DA; Bolotin, DA; Mamedov, IZ; Turchaninova, MA; Putintseva, EV; Kotlobay, AA; Lukyanov, S; Novik, AA; Lebedev, YB; Chudakov, DM, 2012: First autologous hematopoietic SCT for ankylosing spondylitis: a case report and clues to understanding the therapy. BONE MARROW TRANSPLANTATION 47(11), p. 1479 - 1481, doi: 10.1038/bmt.2012.44
• Pletnev, S; Pletneva, NV; Souslova, EA; Chudakov, DM; Lukyanov, S; Wlodawer, A; Dauter, Z; Pletnev, V, 2012: Structural basis for bathochromic shift of fluorescence in far-red fluorescent proteins eqFP650 and eqFP670. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 68, p. 1088 - 1097, doi: 10.1107/S0907444912020598
• Bolotin, DA; Mamedov, IZ; Britanova, OV; Zvyagin, IV; Shagin, D; Ustyugova, SV; Turchaninova, MA; Lukyanov, S; Lebedev, YB; Chudakov, DM, 2012: Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms. EUROPEAN JOURNAL OF IMMUNOLOGY 42(11), p. 3073 - 3083, doi: 10.1002/eji.201242517
• Bolotin, D; Mamedov, I; Britanova, O; van Zvyagin, I; Shagin, D; Ustyugova, S; Turchaninova, M; Lukyanov, S; Lebedev, Y; Chudakov, D, 2012: NEXT GENERATION SEQUENCING FOR TCR REPERTOIRE PROFILING: PLATFORM-SPECIFIC LIBRARY PREPARATION AND DATA ANALYSIS. TISSUE ANTIGENS 79(6), p. 545 - 546
• Britanova, OV; Bolotin, DA; Turchaninova, MA; Mamedov, IZ; Fedorenko, DA; Chudakov, DM, 2012: HEMATOPOIETIC STEM CELL TRANSPLANTATION FOR AUTOIMMUNITY: A CASE REPORT AND CLUES TO UNDERSTANDING THE THERAPY. TISSUE ANTIGENS 79(6), p. 462 - 463
• Luker, KE; Mihalko, LA; Schmidt, BT; Lewin, SA; Ray, P; Shcherbo, D; Chudakov, DM; Luker, GD, 2012: In vivo imaging of ligand receptor binding with Gaussia luciferase cornplementation. NATURE MEDICINE 18(1), p. 172 - 177, doi: 10.1038/nm.2590

2011

• Korzh, V; Teh, C; Kondrychyn, I; Chudakov, DM; Lukyanov, S, 2011: Visualizing Compound Transgenic Zebrafish in Development: A Tale of Green Fluorescent Protein and KillerRed. ZEBRAFISH 8(1), p. 23 - 29, doi: 10.1089/zeb.2011.0689
• Serebrovskaya, EO; Stremovsky, OA; Chudakov, DM; Lukyanov, KA; Deyev, SM, 2011: Genetically Encoded Immunophotosensitizer. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 37(1), p. 123 - 129, doi: 10.1134/S1068162011010134
• Shui, B; Wang, Q; Lee, F; Byrnes, LJ; Chudakov, DM; Lukyanov, SA; Sondermann, H; Kotlikoff, MI, 2011: Circular Permutation of Red Fluorescent Proteins. PLOS ONE 6(5), doi: 10.1371/journal.pone.0020505
• Figueiredo, M; Lane, S; Tang, F; Liu, BH; Hewinson, J; Marina, N; Kasymov, V; Souslova, EA; Chudakov, DM; Gourine, AV; Teschemacher, AG; Kasparov, S, 2011: Optogenetic experimentation on astrocytes. EXPERIMENTAL PHYSIOLOGY 96(1), p. 40 - 50, doi: 10.1113/expphysiol.2010.052597
• Pletneva, NV; Pletnev, VZ; Shemiakina, II; Chudakov, DM; Artemyev, I; Wlodawer, A; Dauter, Z; Pletnev, S, 2011: Crystallographic study of red fluorescent protein eqFP578 and its far-red variant Katushka reveals opposite pH-induced isomerization of chromophore. PROTEIN SCIENCE 20(7), p. 1265 - 1274, doi: 10.1002/pro.654
• Mamedov, IZ; Britanova, OV; Bolotin, DA; Chkalina, AV; Staroverov, DB; Zuyagin, IV; Kotlobay, AA; Turchaninova, MA; Fedorenko, DA; Novik, AA; Sharonov, GV; Lukyanov, S; Chudakov, DM; Lebedev, YB, 2011: Quantitative tracking of T cell clones after haematopoietic stem cell transplantation. EMBO MOLECULAR MEDICINE 3(4), p. 201 - 207, doi: 10.1002/emmm.201100129
• Serebrovskaya, EO; Gorodnicheva, TV; Ermakova, GV; Solovieva, EA; Sharonov, GV; Zagaynova, EV; Chudakov, DM; Lukyanov, S; Zaraisky, AG; Lukyanov, KA, 2011: Light-induced blockage of cell division with a chromatin-targeted phototoxic fluorescent protein. BIOCHEMICAL JOURNAL 435, p. 65 - 71, doi: 10.1042/BJ20101217
• Britanova, OV; Staroverov, DB; Chkalina, AV; Kotlobay, AA; Zvezdova, ES; Bochkova, AG; Chudakov, DM, 2011: Single high-dose treatment with glucosaminyl-muramyl dipeptide is ineffective in treating ankylosing spondylitis. RHEUMATOLOGY INTERNATIONAL 31(8), p. 1101 - 1103, doi: 10.1007/s00296-010-1663-3
• Wang, Q; Byrnes, LJ; Shui, B; Rohrig, UF; Singh, A; Chudakov, DM; Lukyanov, S; Zipfel, WR; Kotlikoff, MI; Sondermann, H, 2011: Molecular Mechanism of a Green-Shifted, pH-Dependent Red Fluorescent Protein mKate Variant. PLOS ONE 6(8), doi: 10.1371/journal.pone.0023513

2010

• Zhang, L; Gurskaya, NG; Kopantseva, YE; Mudrik, NN; Vagner, LL; Lukyanov, KA; Chudakov, DM, 2010: Identification of the amino acid residues responsible for the reversible photoconversion of the monomeric red fluorescent protein TagRFP. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 36(2), p. 179 - 184, doi: 10.1134/S1068162010020068
• Teh, C; Chudakov, DM; Poon, KL; Mamedov, IZ; Sek, JY; Shidlovsky, K; Lukyanov, S; Korzh, V, 2010: Optogenetic in vivo cell manipulation in KillerRed-expressing zebrafish transgenics. BMC DEVELOPMENTAL BIOLOGY 10, doi: 10.1186/1471-213X-10-110
• Zhdanov, AV; Ward, MW; Taylor, CT; Souslova, EA; Chudakov, DM; Prehn, JHM; Papkovsky, DB, 2010: Extracellular calcium depletion transiently elevates oxygen consumption in neurosecretory PC12 cells through activation of mitochondrial Na+/Ca2+ exchange. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1797(8), p. 1627 - 1636, doi: 10.1016/j.bbabio.2010.06.006
• Zvyagin, IV; Mamedov, IZ; Britanova, OV; Staroverov, DB; Nasonov, EL; Bochkova, AG; Chkalina, AV; Kotlobay, AA; Korostin, DO; Rebrikov, DV; Lukyanov, S; Lebedev, YB; Chudakov, DM, 2010: Contribution of functional KIR3DL1 to ankylosing spondylitis. CELLULAR & MOLECULAR IMMUNOLOGY 7(6), p. 471 - 476, doi: 10.1038/cmi.2010.42
• Shcherbo, D; Shemiakina, II; Ryabova, AV; Luker, KE; Schmidt, BT; Souslova, EA; Gorodnicheva, TV; Strukova, L; Shidlovskiy, KM; Britanova, OV; Zaraisky, AG; Lukyanov, KA; Loschenov, VB; Luker, GD; Chudakov, DM, 2010: Near-infrared fluorescent proteins. NATURE METHODS 7(10), p. 827 - U1520, doi: 10.1038/NMETH.1501
• Leder, L; Stark, W; Freuler, F; Marsh, M; Meyerhofer, M; Stettler, T; Mayr, LM; Britanova, OV; Strukova, LA; Chudakov, DM; Souslova, EA, 2010: The Structure of Ca2+ Sensor Case16 Reveals the Mechanism of Reaction to Low Ca2+ Concentrations. SENSORS 10(9), p. 8143 - 8160, doi: 10.3390/s100908143
• Guo, F; Liu, BH; Tang, FG; Lane, S; Souslova, EA; Chudakov, DM; Paton, JFR; Kasparov, S, 2010: Astroglia are a possible cellular substrate of angiotensin(1-7) effects in the rostral ventrolateral medulla. CARDIOVASCULAR RESEARCH 87(3), p. 578 - 584, doi: 10.1093/cvr/cvq059
• Chudakov, DM; Matz, MV; Lukyanov, S; Lukyanov, KA, 2010: Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues. PHYSIOLOGICAL REVIEWS 90(3), p. 1103 - 1163
• Koutsopoulos, OS; Laine, D; Osellame, L; Chudakov, DM; Parton, RG; Frazier, AE; Ryan, MT, 2010: Human Miltons associate with mitochondria and induce microtubule-dependent remodeling of mitochondrial networks. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 1803(5), p. 564 - 574, doi: 10.1016/j.bbamcr.2010.03.006
• Lukyanov, KA; Serebrovskaya, EO; Lukyanov, S; Chudakov, DM, 2010: Fluorescent proteins as light-inducible photochemical partners. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES 9(10), p. 1301 - 1306, doi: 10.1039/c0pp00114g

2009

• Bogdanov, Alexey M.; Bogdanova, Ekaterina A.; Chudakov, Dmitriy M.; Gorodnicheva, Tatiana V.; Lukyanov, Sergey; Lukyanov, Konstantin A., 2009: Cell culture medium affects GFP photostability: a solution. NATURE METHODS 6(12), p. 859 - 860
• Bogdanov, Alexey M.; Mishin, Alexander S.; Yampolsky, Ilia V.; Belousov, Vsevolod V.; Chudakov, Dmitriy M.; Subach, Fedor V.; Verkhusha, Vladislav V.; Lukyanov, Sergey; Lukyanov, Konstantin A., 2009: Green fluorescent proteins are light-induced electron donors. NATURE CHEMICAL BIOLOGY 5(7), p. 459 - 461
• Shcherbo, Dmitry; Souslova, Ekaterina A.; Goedhart, Joachim; Chepurnykh, Tatyana V.; Gaintzeva, Anna; Shemiakina, Irina I.; Gadella, Theodorus W. J.; Lukyanov, Sergey; Chudakov, Dmitriy M., 2009: Practical and reliable FRET/FLIM pair of fluorescent proteins. BMC BIOTECHNOLOGY 9
• 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., 2009: Far-red fluorescent tags for protein imaging in living tissues. BIOCHEMICAL JOURNAL 418, p. 567 - 574
• Mutoh, Hiroki; Perron, Amelie; Dimitrov, Dimitar; Iwamoto, Yuka; Akemann, Walther; Chudakov, Dmitriy M.; Knoepfel, Thomas, 2009: Spectrally-Resolved Response Properties of the Three Most Advanced FRET Based Fluorescent Protein Voltage Probes. PLOS ONE 4(2)

• APERIM - Advanced bioinformatics platform for PERsonalised cancer IMmunotherapy (633592), Evropská unie, 2015 - 2018
• CEITEC - Central European Institute of Technology (CZ.1.05/1.1.00/02.0068), Ministerstvo školství, mládeže a tělovýchovy ČR, 2011 - 2015