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Items: 1 to 50 of 115

1.

Reply to "Evaluation of immune repertoire inference methods from RNA-seq data".

Bolotin DA, Poslavsky S, Davydov AN, Chudakov DM.

Nat Biotechnol. 2018 Nov 9;36(11):1035-1036. doi: 10.1038/nbt.4296. No abstract available.

PMID:
30412204
2.

Comparative Analysis of B-Cell Receptor Repertoires Induced by Live Yellow Fever Vaccine in Young and Middle-Age Donors.

Davydov AN, Obraztsova AS, Lebedin MY, Turchaninova MA, Staroverov DB, Merzlyak EM, Sharonov GV, Kladova O, Shugay M, Britanova OV, Chudakov DM.

Front Immunol. 2018 Oct 9;9:2309. doi: 10.3389/fimmu.2018.02309. eCollection 2018.

3.

CD49b defines functionally mature Treg cells that survey skin and vascular tissues.

Fan X, Moltedo B, Mendoza A, Davydov AN, Faire MB, Mazutis L, Sharma R, Pe'er D, Chudakov DM, Rudensky AY.

J Exp Med. 2018 Nov 5;215(11):2796-2814. doi: 10.1084/jem.20181442. Epub 2018 Oct 24.

PMID:
30355617
4.

Exploring the pre-immune landscape of antigen-specific T cells.

Pogorelyy MV, Fedorova AD, McLaren JE, Ladell K, Bagaev DV, Eliseev AV, Mikelov AI, Koneva AE, Zvyagin IV, Price DA, Chudakov DM, Shugay M.

Genome Med. 2018 Aug 25;10(1):68. doi: 10.1186/s13073-018-0577-7.

5.

The Changing Landscape of Naive T Cell Receptor Repertoire With Human Aging.

Egorov ES, Kasatskaya SA, Zubov VN, Izraelson M, Nakonechnaya TO, Staroverov DB, Angius A, Cucca F, Mamedov IZ, Rosati E, Franke A, Shugay M, Pogorelyy MV, Chudakov DM, Britanova OV.

Front Immunol. 2018 Jul 24;9:1618. doi: 10.3389/fimmu.2018.01618. eCollection 2018.

6.

Optimized Peptide-MHC Multimer Protocols for Detection and Isolation of Autoimmune T-Cells.

Dolton G, Zervoudi E, Rius C, Wall A, Thomas HL, Fuller A, Yeo L, Legut M, Wheeler S, Attaf M, Chudakov DM, Choy E, Peakman M, Sewell AK.

Front Immunol. 2018 Jun 29;9:1378. doi: 10.3389/fimmu.2018.01378. eCollection 2018.

7.

Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy.

Pennacchietti F, Serebrovskaya EO, Faro AR, Shemyakina II, Bozhanova NG, Kotlobay AA, Gurskaya NG, Bodén A, Dreier J, Chudakov DM, Lukyanov KA, Verkhusha VV, Mishin AS, Testa I.

Nat Methods. 2018 Aug;15(8):601-604. doi: 10.1038/s41592-018-0052-9. Epub 2018 Jul 9.

PMID:
29988095
8.

Human liver infiltrating γδ T cells are composed of clonally expanded circulating and tissue-resident populations.

Hunter S, Willcox CR, Davey MS, Kasatskaya SA, Jeffery HC, Chudakov DM, Oo YH, Willcox BE.

J Hepatol. 2018 Sep;69(3):654-665. doi: 10.1016/j.jhep.2018.05.007. Epub 2018 May 18.

9.

The human Vδ2+ T-cell compartment comprises distinct innate-like Vγ9+ and adaptive Vγ9- subsets.

Davey MS, Willcox CR, Hunter S, Kasatskaya SA, Remmerswaal EBM, Salim M, Mohammed F, Bemelman FJ, Chudakov DM, Oo YH, Willcox BE.

Nat Commun. 2018 May 2;9(1):1760. doi: 10.1038/s41467-018-04076-0.

10.

Method for identification of condition-associated public antigen receptor sequences.

Pogorelyy MV, Minervina AA, Chudakov DM, Mamedov IZ, Lebedev YB, Mora T, Walczak AM.

Elife. 2018 Mar 13;7. pii: e33050. doi: 10.7554/eLife.33050.

11.

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

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.

Rheumatology (Oxford). 2018 Jun 1;57(6):1097-1104. doi: 10.1093/rheumatology/kex517.

PMID:
29481668
12.

Quantitative profiling reveals minor changes of T cell receptor repertoire in response to subunit inactivated influenza vaccine.

Sycheva AL, Pogorelyy MV, Komech EA, Minervina AA, Zvyagin IV, Staroverov DB, Chudakov DM, Lebedev YB, Mamedov IZ.

Vaccine. 2018 Mar 14;36(12):1599-1605. doi: 10.1016/j.vaccine.2018.02.027. Epub 2018 Feb 15.

PMID:
29454515
13.

Comparative analysis of murine T-cell receptor repertoires.

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.

Immunology. 2018 Feb;153(2):133-144. doi: 10.1111/imm.12857. Epub 2017 Nov 27. Review.

PMID:
29080364
14.

Antigen receptor repertoire profiling from RNA-seq data.

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.

Nat Biotechnol. 2017 Oct 11;35(10):908-911. doi: 10.1038/nbt.3979. No abstract available.

15.

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

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.

Nucleic Acids Res. 2018 Jan 4;46(D1):D419-D427. doi: 10.1093/nar/gkx760.

16.

Corrigendum: Stability and function of regulatory T cells expressing the transcription factor T-bet.

Levine AG, Mendoza 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.

Nature. 2017 Sep 20;550(7674):142. doi: 10.1038/nature24013.

PMID:
28953866
17.

Insertion of the voltage-sensitive domain into circularly permuted red fluorescent protein as a design for genetically encoded voltage sensor.

Kost LA, Nikitin ES, Ivanova VO, Sung U, Putintseva EV, Chudakov DM, Balaban PM, Lukyanov KA, Bogdanov AM.

PLoS One. 2017 Sep 1;12(9):e0184225. doi: 10.1371/journal.pone.0184225. eCollection 2017.

18.

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

Pogorelyy MV, Elhanati Y, Marcou Q, Sycheva AL, Komech EA, Nazarov VI, Britanova OV, Chudakov DM, Mamedov IZ, Lebedev YB, Mora T, Walczak AM.

PLoS Comput Biol. 2017 Jul 6;13(7):e1005572. doi: 10.1371/journal.pcbi.1005572. eCollection 2017 Jul.

19.

Stability and function of regulatory T cells expressing the transcription factor T-bet.

Levine AG, Mendoza 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.

Nature. 2017 Jun 15;546(7658):421-425. doi: 10.1038/nature22360. Epub 2017 Jun 7. Erratum in: Nature. 2017 Sep 20;:.

20.

Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries.

Shagin DA, Turchaninova MA, Shagina IA, Shugay M, Zaretsky AR, Zueva OI, Bolotin DA, Lukyanov S, Chudakov DM.

BMC Genomics. 2017 Jun 5;18(1):440. doi: 10.1186/s12864-017-3815-2.

21.

A high-throughput assay for quantitative measurement of PCR errors.

Shagin DA, Shagina IA, Zaretsky AR, Barsova EV, Kelmanson IV, Lukyanov S, Chudakov DM, Shugay M.

Sci Rep. 2017 Jun 2;7(1):2718. doi: 10.1038/s41598-017-02727-8.

22.

MAGERI: Computational pipeline for molecular-barcoded targeted resequencing.

Shugay M, Zaretsky AR, Shagin DA, Shagina IA, Volchenkov IA, Shelenkov AA, Lebedin MY, Bagaev DV, Lukyanov S, Chudakov DM.

PLoS Comput Biol. 2017 May 5;13(5):e1005480. doi: 10.1371/journal.pcbi.1005480. eCollection 2017 May.

23.

Clonal selection in the human Vδ1 T cell repertoire indicates γδ TCR-dependent adaptive immune surveillance.

Davey MS, Willcox CR, Joyce SP, Ladell K, Kasatskaya SA, McLaren JE, Hunter S, Salim M, Mohammed F, Price DA, Chudakov DM, Willcox BE.

Nat Commun. 2017 Mar 1;8:14760. doi: 10.1038/ncomms14760.

24.

Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer.

Plitas G, Konopacki C, Wu K, Bos PD, Morrow M, Putintseva EV, Chudakov DM, Rudensky AY.

Immunity. 2016 Nov 15;45(5):1122-1134. doi: 10.1016/j.immuni.2016.10.032.

25.

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

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.

Leukemia. 2017 May;31(5):1145-1153. doi: 10.1038/leu.2016.321. Epub 2016 Nov 4.

PMID:
27811849
26.

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

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.

Nat Protoc. 2016 Sep;11(9):1599-616. doi: 10.1038/nprot.2016.093. Epub 2016 Aug 4.

PMID:
27490633
27.

Single-cell analysis of glandular T cell receptors in Sjögren's syndrome.

Joachims ML, Leehan KM, Lawrence C, Pelikan RC, Moore JS, Pan Z, 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.

JCI Insight. 2016 Jun 2;1(8). pii: e85609.

28.

VDJviz: a versatile browser for immunogenomics data.

Bagaev DV, Zvyagin IV, Putintseva EV, Izraelson M, Britanova OV, Chudakov DM, Shugay M.

BMC Genomics. 2016 Jun 13;17:453. doi: 10.1186/s12864-016-2799-7.

29.

Reliability of immune receptor rearrangements as genetic markers for minimal residual disease monitoring.

Nazarov VI, Minervina AA, Komkov AY, Pogorelyy MV, Maschan MA, Olshanskaya YV, Zvyagin IV, Chudakov DM, Lebedev YB, Mamedov IZ.

Bone Marrow Transplant. 2016 Oct;51(10):1408-1410. doi: 10.1038/bmt.2016.148. Epub 2016 May 23. No abstract available.

PMID:
27214078
30.

Local fitness landscape of the green fluorescent protein.

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.

Nature. 2016 May 19;533(7603):397-401. doi: 10.1038/nature17995. Epub 2016 May 11.

31.

Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians.

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.

J Immunol. 2016 Jun 15;196(12):5005-13. doi: 10.4049/jimmunol.1600005. Epub 2016 May 13.

32.

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.

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.

PLoS Comput Biol. 2015 Nov 25;11(11):e1004503. doi: 10.1371/journal.pcbi.1004503. eCollection 2015 Nov.

33.

A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance.

Feng Y, 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.

Nature. 2015 Dec 3;528(7580):132-136. doi: 10.1038/nature16141. Epub 2015 Nov 25.

34.

Sequencing rare T-cell populations.

Shugay M, Lukyanov S, Chudakov DM.

Oncotarget. 2015 Nov 24;6(37):39393-4. doi: 10.18632/oncotarget.6349. No abstract available.

35.

TCR usage, gene expression and function of two distinct FOXP3(+)Treg subsets within CD4(+)CD25(hi) T cells identified by expression of CD39 and CD45RO.

Ye L, Goodall JC, Zhang L, Putintseva EV, Lam B, Jiang L, Liu W, Yin J, Lin L, Li T, Wu X, Yeo G, Shugay M, Chudakov DM, Gaston H, Xu H.

Immunol Cell Biol. 2016 Mar;94(3):293-305. doi: 10.1038/icb.2015.90. Epub 2015 Oct 15.

PMID:
26467610
36.

Comparative study reveals better far-red fluorescent protein for whole body imaging.

Luker KE, Pata P, Shemiakina II, Pereverzeva A, Stacer AC, Shcherbo DS, Pletnev VZ, Skolnaja M, Lukyanov KA, Luker GD, Pata I, Chudakov DM.

Sci Rep. 2015 Jun 2;5:10332. doi: 10.1038/srep10332.

37.

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

Nazarov VI, Pogorelyy MV, Komech EA, Zvyagin IV, Bolotin DA, Shugay M, Chudakov DM, Lebedev YB, Mamedov IZ.

BMC Bioinformatics. 2015 May 28;16:175. doi: 10.1186/s12859-015-0613-1.

38.

Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers.

Egorov ES, Merzlyak EM, Shelenkov AA, Britanova OV, Sharonov GV, Staroverov DB, Bolotin DA, Davydov AN, Barsova E, Lebedev YB, Shugay M, Chudakov DM.

J Immunol. 2015 Jun 15;194(12):6155-63. doi: 10.4049/jimmunol.1500215. Epub 2015 May 8.

39.

MiXCR: software for comprehensive adaptive immunity profiling.

Bolotin DA, Poslavsky S, Mitrophanov I, Shugay M, Mamedov IZ, Putintseva EV, Chudakov DM.

Nat Methods. 2015 May;12(5):380-1. doi: 10.1038/nmeth.3364. No abstract available.

PMID:
25924071
40.

Experimental models of arthritis in which pathogenesis is dependent on TNF expression.

Drutskaya MS, Efimov GA, Zvartsev RV, Chashchina AA, Chudakov DM, Tillib SV, Kruglov AA, Nedospasov SA.

Biochemistry (Mosc). 2014 Dec;79(12):1349-57. doi: 10.1134/S0006297914120086.

41.

Towards error-free profiling of immune repertoires.

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.

Nat Methods. 2014 Jun;11(6):653-5. doi: 10.1038/nmeth.2960. Epub 2014 May 4.

PMID:
24793455
42.

Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing.

Zvyagin IV, Pogorelyy MV, Ivanova ME, Komech EA, Shugay M, Bolotin DA, Shelenkov AA, Kurnosov AA, Staroverov DB, Chudakov DM, Lebedev YB, Mamedov IZ.

Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5980-5. doi: 10.1073/pnas.1319389111. Epub 2014 Apr 7.

43.

Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling.

Britanova OV, Putintseva EV, Shugay M, Merzlyak EM, Turchaninova MA, Staroverov DB, Bolotin DA, Lukyanov S, Bogdanova EA, Mamedov IZ, Lebedev YB, Chudakov DM.

J Immunol. 2014 Mar 15;192(6):2689-98. doi: 10.4049/jimmunol.1302064. Epub 2014 Feb 7.

44.

HRES-1/Rab4 promotes the formation of LC3(+) autophagosomes and the accumulation of mitochondria during autophagy.

Talaber G, Miklossy G, Oaks Z, Liu Y, Tooze SA, Chudakov DM, Banki K, Perl A.

PLoS One. 2014 Jan 3;9(1):e84392. doi: 10.1371/journal.pone.0084392. eCollection 2014.

45.

Huge Overlap of Individual TCR Beta Repertoires.

Shugay M, Bolotin DA, Putintseva EV, Pogorelyy MV, Mamedov IZ, Chudakov DM.

Front Immunol. 2013 Dec 25;4:466. doi: 10.3389/fimmu.2013.00466. eCollection 2013. No abstract available.

46.

Mother and child T cell receptor repertoires: deep profiling study.

Putintseva EV, Britanova OV, Staroverov DB, Merzlyak EM, Turchaninova MA, Shugay M, Bolotin DA, Pogorelyy MV, Mamedov IZ, Bobrynina V, Maschan M, Lebedev YB, Chudakov DM.

Front Immunol. 2013 Dec 25;4:463. doi: 10.3389/fimmu.2013.00463. eCollection 2013.

47.

Preparing unbiased T-cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling.

Mamedov IZ, Britanova OV, Zvyagin IV, Turchaninova MA, Bolotin DA, Putintseva EV, Lebedev YB, Chudakov DM.

Front Immunol. 2013 Dec 23;4:456. doi: 10.3389/fimmu.2013.00456. eCollection 2013.

48.

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

Linnemann C, Heemskerk B, Kvistborg P, Kluin RJ, Bolotin DA, Chen X, 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 JB, Turchaninova MA, Kerkhoven RM, Spits H, Hadrup SR, Heemskerk MH, Blankenstein T, Chudakov DM, Bendle GM, Schumacher TN.

Nat Med. 2013 Nov;19(11):1534-41. doi: 10.1038/nm.3359. Epub 2013 Oct 13.

PMID:
24121928
49.

Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine.

Pletnev VZ, Pletneva NV, Lukyanov KA, Souslova EA, Fradkov AF, Chudakov DM, Chepurnykh T, Yampolsky IV, Wlodawer A, Dauter Z, Pletnev S.

Acta Crystallogr D Biol Crystallogr. 2013 Sep;69(Pt 9):1850-60. doi: 10.1107/S0907444913015424. Epub 2013 Aug 17.

50.

HRES-1/Rab4-mediated depletion of Drp1 impairs mitochondrial homeostasis and represents a target for treatment in SLE.

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.

Ann Rheum Dis. 2014 Oct;73(10):1888-97. doi: 10.1136/annrheumdis-2013-203794. Epub 2013 Jul 29.

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