Шагин Дмитрий Алексеевич

Кандидат биологических наук


Старший инженер (Лаборатория биофотоники)

Эл. почта: shagdim@evrogen.ru

Избранные публикации

  1. Kostin NN, Bobik TV, Shurdova EM, Ziganshin RH, Surina EA, Shagin DA, Shagina IA, Knorre VD, Isaev VA, Rudenskaya GN, Gabibov AG, Smirnov IV (2018). Cloning and characterization of serpin from red king crab Paralithodes camtschaticus. Fish Shellfish Immunol 81 (0), 99–107
  2. Arbatsky NP, Shneider MM, Dmitrenok AS, Popova AV, Shagin DA, Shelenkov AA, Mikhailova YV, Edelstein MV, Knirel YA (2018). Structure and gene cluster of the K125 capsular polysaccharide from Acinetobacter baumannii MAR13-1452. Int J Biol Macromol 117 (0), 1195–1199
  3. 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. Sci Rep 7 (1), 2718
  4. 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 (1), 440
  5. 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 Comput Biol 13 (5), e1005480
  6. 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. Nat Methods 11 (6), 653–655
  7. Goptar IA, Shagin DA, Shagina IA, Mudrik ES, Smirnova YA, Zhuzhikov DP, Belozersky MA, Dunaevsky YE, Oppert B, Filippova IY, Elpidina EN (2013). A digestive prolyl carboxypeptidase in Tenebrio molitor larvae. Insect Biochem Mol Biol 43 (6), 501–509
  8. Petzold A, Reichwald K, Groth M, Taudien S, Hartmann N, Priebe S, Shagin D, Englert C, Platzer M (2013). The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels. BMC Genomics 14 (1), 185
  9. 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. Eur J Immunol 42 (11), 3073–3083
  10. Kirschner J, Weber D, Neuschl C, Franke A, Böttger M, Zielke L, Powalsky E, Groth M, Shagin D, Petzold A, Hartmann N, Englert C, Brockmann GA, Platzer M, Cellerino A, Reichwald K (2012). Mapping of quantitative trait loci controlling lifespan in the short-lived fish Nothobranchius furzeri- a new vertebrate model for age research. Aging Cell 11 (2), 252–261
  11. Kurnikova M, Maschan M, Dinova E, Shagina I, Finogenova N, Mamedova E, Polovtseva T, Shagin D, Shcherbina A (2011). Four novel ELANE mutations in patients with congenital neutropenia. Pediatr Blood Cancer 57 (2), 332–335
  12. Shagina IA, Bogdanova EA, Altshuler IM, Lukyanov SA, Shagin DA (2011). The use of duplex-specific crab nuclease for rapid analysis of single-nucleotide polymorphisms and the detection of dna targets in complex PCR products. Russ. J. Bioorganic Chem. 37 (4), 464–471
  13. Bogdanova EA, Barsova EV, Shagina IA, Scheglov A, Anisimova V, Vagner LL, Lukyanov SA, Shagin DA (2011). Normalization of full-length-enriched cDNA. Methods Mol Biol 729 (0), 85–98
  14. Kurnikova M, Dinova E, Shagina I, Shagin D (2011). Alu-mediated recombination in the HAX1 gene as the molecular basis of severe congenital neutropenia. Am J Med Genet A 155 (3), 660–661
  15. Mamedov IZ, Shagina IA, Kurnikova MA, Novozhilov SN, Shagin DA, Lebedev YB (2010). A new set of markers for human identification based on 32 polymorphic Alu insertions. Eur J Hum Genet 18 (7), 808–814
  16. Bogdanov EA, Shagina I, Barsova EV, Kelmanson I, Shagin DA, Lukyanov SA (2010). Normalizing cDNA libraries. Curr Protoc Mol Biol  (90), Unit 5.12.1–27
  17. Shagina I, Bogdanova E, Mamedov IZ, Lebedev Y, Lukyanov S, Shagin D (2010). Normalization of genomic DNA using duplex-specific nuclease. Biotechniques 48 (6), 455–459
  18. 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 (2009). Individual characterization of stably expanded T cell clones in ankylosing spondylitis patients. Autoimmunity 42 (6), 525–536
  19. Bogdanova EA, Shagina IA, Mudrik E, Ivanov I, Amon P, Vagner LL, Lukyanov SA, Shagin DA (2009). DSN depletion is a simple method to remove selected transcripts from cDNA populations. Mol Biotechnol 41 (3), 247–253
  20. Kurnikova M, Shagina I, Khachatryan L, Schagina O, Maschan M, Shagin D (2009). Identification of a novel mutation in DKC1 in dyskeratosis congenita. Pediatr Blood Cancer 52 (1), 135–137
  21. Anisimova VE, Shcheglov AS, Bogdanova EA, Rebrikov DV, Nekrasov AN, Barsova EV, Shagin DA, Lukyanov SA (2008). Is crab duplex-specific nuclease a member of the Serratia family of non-specific nucleases? Gene 418 (12), 41–48
  22. Anisimova VE, Rebrikov DV, Shagin DA, Kozhemyako VB, Menzorova NI, Staroverov DB, Ziganshin R, Vagner LL, Rasskazov VA, Lukyanov SA, Shcheglov AS (2008). Isolation, characterization and molecular cloning of Duplex-Specific Nuclease from the hepatopancreas of the Kamchatka crab. BMC Biochem 9 (1), 14
  23. Schostak N, Pyatkov K, Zelentsova E, Arkhipova I, Shagin D, Shagina I, Mudrik E, Blintsov A, Clark I, Finnegan DJ, Evgenev M (2008). Molecular dissection of Penelope transposable element regulatory machinery. Nucleic Acids Res 36 (8), 2522–2529
  24. Bogdanova EA, Shagin DA, Lukyanov SA (2008). Normalization of full-length enriched cDNA. Mol Biosyst 4 (3), 205–212
  25. Gonchar DA, Abdurashitov MA, Okhapkina SS, Shagin DA, Kileva EV, Degtyarev SK (2007). Sse9I restriction-modification system: Organization of genes and structural comparison of proteins. Mol Biol 41 (3), 438–444
  26. Shcheglov AS, Zhulidov PA, Bogdanova EA, Shagin DA (2007). Normalization of cDNA libraries.  (0), 97–124
  27. Altshuler IM, Zhulidov PA, Bogdanova EA, Mudrik NN, Shagin DA (2005). Application of the duplex-specific nuclease preference method to the analysis of single nucleotide polymorphisms in human genes. Bioorg Khim 31 (6), 627–636
  28. Zhulidov PA, Bogdanova EA, Shcheglov AS, Shagina IA, Wagner LL, Khazpekov GL, Kozhemyako VV, Lukyanov SA, Shagin DA (2005). A method for the preparation of normalized cDNA libraries enriched with full-length sequences. Bioorg Khim 31 (2), 186–194
  29. Altshuler IM, Zhulidov PA, Bogdanova EA, Mudrik NN, Shagin DA (2005). Application of the duplex-specific nuclease preference method to the analysis of single nucleotide polymorphisms in human genes. Russ. J. Bioorganic Chem. 31 (6), 567–575
  30. Zhulidov PA, Bogdanova EA, Shcheglov AS, Shagina IA, Wagner LL, Khazpekov GL, Kozhemyako VV, Lukyanov SA, Shagin DA (2005). A method for the preparation of normalized cDNA libraries enriched with full-length sequences. Russ. J. Bioorganic Chem. 31 (2), 170–177
  31. Yanushevich YG, Shagin DA, Fradkov AF, Shakhbazov KS, Barsova EV, Gurskaya NG, Labas YA, Matz MV, Lukyanov KA, Lukyanov SA (2005). Spectral diversity among members of the green fluorescent protein family in hydroid jellyfish (Cnidaria, Hydrozoa). Russ. J. Bioorganic Chem. 31 (1), 43–47
  32. Diatchenko L, Slade GD, Nackley AG, Bhalang K, Sigurdsson A, Belfer I, Goldman D, Xu K, Shabalina SA, Shagin D, Max MB, Makarov SS, Maixner W (2005). Genetic basis for individual variations in pain perception and the development of a chronic pain condition. Hum Mol Genet 14 (1), 135–143
  33. Bogdanova EA, Barsova EV, Punkova NI, Britanova OV, Shagin DA, Gurskaya NG, Usman NY, Lukyanov SA (2004). A family of genes of multidomain free lectins from a planarian: Structure, expression, and the use as markers for monitoring regeneration. Russ. J. Bioorganic Chem. 30 (6), 566–576
  34. Zhulidov PA, Bogdanova EA, Shcheglov AS, Vagner LL, Khaspekov GL, Kozhemyako VB, Matz MV, Meleshkevitch E, Moroz LL, Lukyanov SA, Shagin DA (2004). Simple cDNA normalization using kamchatka crab duplex-specific nuclease. Nucleic Acids Res 32 (3), e37
  35. Shagin DA, Barsova EV, Yanushevich YG, Fradkov AF, Lukyanov KA, Labas YA, Semenova TN, Ugalde JA, Meyers A, Nunez JM, Widder EA, Lukyanov SA, Matz MV (2004). GFP-like Proteins as Ubiquitous Metazoan Superfamily: Evolution of Functional Features and Structural Complexity. Mol Biol Evol 21 (5), 841–850
  36. Baranova A, Ivanov D, Petrash N, Pestova A, Skoblov M, Kelmanson I, Shagin D, Nazarenko S, Geraymovych E, Litvin O, Tiunova A, Born TL, Usman N, Staroverov D, Lukyanov S, Panchin Y (2004). The mammalian pannexin family is homologous to the invertebrate innexin gap junction proteins. Genomics 83 (4), 706–716
  37. Baranova A, Hammarsund M, Ivanov D, Skoblov M, Sangfelt O, Corcoran M, Borodina T, Makeeva N, Pestova A, Tyazhelova T, Nazarenko S, Gorreta F, Alsheddi T, Schlauch K, Nikitin E, Kapanadze B, Shagin D, Poltaraus A, Vorobiev AI, Zabarovsky E, Lukianov S, Chandhoke V, Ibbotson R, Oscier D, Einhorn S, Grander D, Yankovsky N (2003). Distinct organization of the candidate tumor suppressor gene RFP2 in human and mouse: Multiple mRNA isoforms in both species- and human-specific antisense transcript RFP2OS. Gene 321 (12), 103–112
  38. Kelmanson IV, Shagin DA, Usman N, Matz MV, Lukyanov SA, Panchin YV (2002). Altering electrical connections in the nervous system of the pteropod mollusc Clione limacina by neuronal injections of gap junction mRNA. Eur J Neurosci 16 (12), 2475–2476
  39. Shagin DA, Rebrikov DV, Kozhemyako VB, Altshuler IM, Shcheglov AS, Zhulidov PA, Bogdanova EA, Staroverov DB, Rasskazov VA, Lukyanov S (2002). A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas. Genome Res 12 (12), 1935–1942
  40. Shagin DA, Barsova EV, Bogdanova EA, Britanova OV, Gurskaya NG, Lukyanov KA, Matz MV, Punkova NI, Usman NY, Kopantzev EP, Salo E, Lukyanov SA (2002). Identification and characterization of a new family of C-type lectin-like genes from planaria Girardia tigrina. Glycobiology 12 (8), 463–472
  41. Shagin DA, Lukyanov KA, Vagner LL, Matz MV (1999). Regulation of average length of complex PCR product. Nucleic Acids Res 27 (18), e23
  42. Matz M, Shagin D, Bogdanova E, Britanova O, Lukyanov S, Diatchenko L, Chenchik A (1999). Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res 27 (6), 1558–1560
  43. Matz MV, Shagin DA, Usman NY, Bogdanova EA, Fradkov AF, Soboleva TA, Lukyanov SA (1998). Cloning of Region-Specific Genetic Markers of Planarian Dugesia tigrina by Means of a New Method: Ordered Differential Display. Bioorg Khim 24 (12), 915
  44. Mats MV, Shagin DA, Usman NI, Bogdanova EA, Fradkov AF, Soboleva TA, Lukianov SA (1998). Cloning of region-specific genetic markers of planaria using a new method--ordered differential display. Bioorg Khim 24 (12), 910–915
  45. Matz MV, Shagin DA, Usman NY, Bogdanova EA, Fradkov AF, Soboleva TA, Lukyanov SA (1998). Cloning of region-specific genetic markers of planarian Dugesia tigrina by means of a new method: Ordered differential display. Russ. J. Bioorganic Chem. 24 (12), 808–812
  46. Bogdanova E, Matz M, Tarabykin V, Usman N, Shagin D, Zaraisky A, Lukyanov S (1998). Inductive interactions regulating body patterning in planarian, revealed by analysis of expression of novel gene scarf. Dev Biol 194 (2), 172–181
  47. Matz M, Usman N, Shagin D, Bogdanova E, Lukyanov S (1997). Ordered differential display: A simple method for systematic comparison of gene expression profiles. Nucleic Acids Res 25 (12), 2541–2542
  48. Gurskaya NG, Shagin DA, Lukyanov KA, Vagner LL, Shtutman MS, Musatkina EA, Moinova EV, Tatosyan AG, Lukyanov SA, Sverdlov ED (1996). Cloning of the ha-SDGF gene cDNA from a highly metastatic golden hamster cell line by subtractive hybridization. Russ. J. Bioorganic Chem. 22 (6), 368–373
  49. Gurskaya NG, Shagin DA, Lukyanov KA, Vagner LL, Shtutman MS, Musatkina EA, Moinova EV, Tatosyan AG, Lukyanov SA, Sverdlov ED (1996). Cloning of the ha-SDGF Gene cDNA from a Highly Metastatic Golden Hamster Cell Line by Subtractive Hybridization. Bioorg Khim 22 (6), 430–431