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Items: 43

1.

Detecting T cell receptors involved in immune responses from single repertoire snapshots.

Pogorelyy MV, Minervina AA, Shugay M, Chudakov DM, Lebedev YB, Mora T, Walczak AM.

PLoS Biol. 2019 Jun 13;17(6):e3000314. doi: 10.1371/journal.pbio.3000314. eCollection 2019 Jun.

2.

[A Pipeline for the Error-free Identification of Somatic Alu Insertions in High-throughput Sequencing Data].

Nugmanov GA, Komkov AY, Saliutina MV, Minervina AA, Lebedev YB, Mamedov IZ.

Mol Biol (Mosk). 2019 Jan-Feb;53(1):154-165. doi: 10.1134/S0026898419010117. Russian.

3.

Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins.

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.

Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):12704-12709. doi: 10.1073/pnas.1809642115. Epub 2018 Nov 20.

4.

An advanced enrichment method for rare somatic retroelement insertions sequencing.

Komkov AY, Minervina AA, Nugmanov GA, Saliutina MV, Khodosevich KV, Lebedev YB, Mamedov IZ.

Mob DNA. 2018 Oct 31;9:31. doi: 10.1186/s13100-018-0136-1. eCollection 2018.

5.

Characterization of the T-cell Repertoire after Autologous HSCT in Patients with Ankylosing Spondylitis.

Komech EA, Zvyagin IV, Pogorelyy MV, Mamedov IZ, Fedorenko DA, Lebedev YB.

Acta Naturae. 2018 Apr-Jun;10(2):48-57.

6.

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.

7.

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
8.

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
9.

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.

10.

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
11.

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
12.

Advanced lymphoblastic clones detection in T-cell leukemia.

Minervina AA, Komkov AY, Mamedov IZ, Lebedev YB.

Dokl Biochem Biophys. 2016 Mar;467(1):85-8. doi: 10.1134/S1607672916020022. Epub 2016 May 20.

PMID:
27193704
13.

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.

14.

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.

15.

The evidence for increased L1 activity in the site of human adult brain neurogenesis.

Kurnosov AA, Ustyugova SV, Nazarov VI, Minervina AA, Komkov AY, Shugay M, Pogorelyy MV, Khodosevich KV, Mamedov IZ, Lebedev YB.

PLoS One. 2015 Feb 17;10(2):e0117854. doi: 10.1371/journal.pone.0117854. eCollection 2015.

16.

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.

17.

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.

18.

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.

19.

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.

20.

Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms.

Bolotin DA, Mamedov IZ, Britanova OV, Zvyagin IV, Shagin D, Ustyugova SV, Turchaninova MA, Lukyanov S, Lebedev YB, Chudakov DM.

Eur J Immunol. 2012 Nov;42(11):3073-83. doi: 10.1002/eji.201242517. Epub 2012 Sep 24.

21.

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

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.

Bone Marrow Transplant. 2012 Nov;47(11):1479-81. doi: 10.1038/bmt.2012.44. Epub 2012 Mar 12. No abstract available.

PMID:
22410749
22.

Quantitative tracking of T cell clones after haematopoietic stem cell transplantation.

Mamedov IZ, Britanova OV, Bolotin DA, Chkalina AV, Staroverov DB, Zvyagin IV, Kotlobay AA, Turchaninova MA, Fedorenko DA, Novik AA, Sharonov GV, Lukyanov S, Chudakov DM, Lebedev YB.

EMBO Mol Med. 2011 Apr;3(4):201-7. doi: 10.1002/emmm.201100129. Epub 2011 Mar 4.

23.

Contribution of functional KIR3DL1 to ankylosing spondylitis.

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.

Cell Mol Immunol. 2010 Nov;7(6):471-6. doi: 10.1038/cmi.2010.42. Epub 2010 Sep 6.

24.

Association of ERAP1 Allelic Variants with Risk of Ankylosing Spondylitis.

Zvyagin IV, Dorodnykh VY, Mamedov IZ, Staroverov DB, Bochkova AG, Rebrikov DV, Lebedev YB.

Acta Naturae. 2010 Jul;2(3):72-7.

25.

A new set of markers for human identification based on 32 polymorphic Alu insertions.

Mamedov IZ, Shagina IA, Kurnikova MA, Novozhilov SN, Shagin DA, Lebedev YB.

Eur J Hum Genet. 2010 Jul;18(7):808-14. doi: 10.1038/ejhg.2010.22. Epub 2010 Feb 24.

26.

Individual characterization of stably expanded T cell clones in ankylosing spondylitis patients.

Mamedov IZ, Britanova OV, Chkalina AV, Staroverov DB, Amosova AL, Mishin AS, Kurnikova MA, Zvyagin IV, Mutovina ZY, Gordeev AV, Khaidukov SV, Sharonov GV, Shagin DA, Chudakov DM, Lebedev YB.

Autoimmunity. 2009 Sep;42(6):525-36. doi: 10.1080/08916930902960362.

PMID:
19657773
27.

Human trash ESTs--sequences from cDNA collection that are not aligned to genome assembly.

Panchin AY, Spirin SA, Lukyanov SA, Lebedev YB, Panchin YV.

J Bioinform Comput Biol. 2008 Aug;6(4):759-73.

PMID:
18763741
28.

Most recent AluY insertions in human gene introns reduce the content of the primary transcripts in a cell type specific manner.

Lebedev YB, Amosova AL, Mamedov IZ, Fisunov GY, Sverdlov ED.

Gene. 2007 Apr 1;390(1-2):122-9. Epub 2006 Oct 17.

PMID:
17118582
29.

Long L1 insertions in human gene introns specifically reduce the content of corresponding primary transcripts.

Ustyugova SV, Lebedev YB, Sverdlov ED.

Genetica. 2006 Sep-Nov;128(1-3):261-72.

PMID:
17028956
30.

Cell line fingerprinting using retroelement insertion polymorphism.

Ustyugova SV, Amosova AL, Lebedev YB, Sverdlov ED.

Biotechniques. 2005 Apr;38(4):561-5.

31.

Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach.

Mamedov IZ, Arzumanyan ES, Amosova AL, Lebedev YB, Sverdlov ED.

Nucleic Acids Res. 2005 Jan 26;33(2):e16.

32.
33.

Identification of paralogous HERV-K LTRs on human chromosomes 3, 4, 7 and 11 in regions containing clusters of olfactory receptor genes.

Nadezhdin EV, Lebedev YB, Glazkova DV, Bornholdt D, Arman IP, Grzeschik KH, Hunsmann G, Sverdlov ED.

Mol Genet Genomics. 2001 Jul;265(5):820-5.

PMID:
11523799
34.

Full-sized HERV-K (HML-2) human endogenous retroviral LTR sequences on human chromosome 21: map locations and evolutionary history.

Kurdyukov SG, Lebedev YB, Artamonova II, Gorodentseva TN, Batrak AV, Mamedov IZ, Azhikina TL, Legchilina SP, Efimenko IG, Gardiner K, Sverdlov ED.

Gene. 2001 Jul 25;273(1):51-61.

PMID:
11483360
35.

Solitary HERV-K LTRs possess bi-directional promoter activity and contain a negative regulatory element in the U5 region.

Domansky AN, Kopantzev EP, Snezhkov EV, Lebedev YB, Leib-Mosch C, Sverdlov ED.

FEBS Lett. 2000 Apr 28;472(2-3):191-5.

36.

Differences in HERV-K LTR insertions in orthologous loci of humans and great apes.

Lebedev YB, Belonovitch OS, Zybrova NV, Khil PP, Kurdyukov SG, Vinogradova TV, Hunsmann G, Sverdlov ED.

Gene. 2000 Apr 18;247(1-2):265-77.

PMID:
10773466
37.

Identification and localization of differences between Escherichia coli and Salmonella typhimurium genomes by suppressive subtractive hybridization.

Bogush ML, Velikodvorskaya TV, Lebedev YB, Nikolaev LG, Lukyanov SA, Fradkov AF, Pliyev BK, Boichenko MN, Usatova GN, Vorobiev AA, Andersen GL, Sverdlov ED.

Mol Gen Genet. 1999 Dec;262(4-5):721-9.

PMID:
10628854
38.

Fine mapping of a polymorphic CA repeat marker on human chromosome 19 and its use in population studies.

Belyaeva OV, Balanovsky OP, Ashworth LK, Lebedev YB, Spitsyn VA, Guseva NA, Erdes S, Mikulich AI, Khusnutdinova EK, Limborska SA.

Gene. 1999 Apr 16;230(2):259-66.

PMID:
10216265
40.

High resolution mapping DNAs by R-loop atomic force microscopy.

Klinov DV, Lagutina IV, Prokhorov VV, Neretina T, Khil PP, Lebedev YB, Cherny DI, Demin VV, Sverdlov ED.

Nucleic Acids Res. 1998 Oct 15;26(20):4603-10.

41.

Long terminal repeats of human endogenous retrovirus K family (HERV-K) specifically bind host cell nuclear proteins.

Akopov SB, Nikolaev LG, Khil PP, Lebedev YB, Sverdlov ED.

FEBS Lett. 1998 Jan 16;421(3):229-33.

42.

Physical mapping of sequences homologous to an endogenous retrovirus LTR on human chromosome 19.

Lebedev YB, Volik SV, Obradovic D, Ermolaeva OD, Ashworth LK, Lennon GG, Sverdlov ED.

Mol Gen Genet. 1995 Jun 25;247(6):742-8.

PMID:
7616966
43.

Conversion of differentiation inducer resistance to differentiation inducer sensitivity in erythroleukemia cells.

Michaeli J, Lebedev YB, Richon VM, Chen ZX, Marks PA, Rifkind RA.

Mol Cell Biol. 1990 Jul;10(7):3535-40.

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