Our recent publications

2020

• Juris Jansons, Ekaterina Bayurova, Dace Skrastina, Alisa Kurlanda, Ilze Fridrihsone, Dmitry Kostyushev, Anastasia Kostyusheva, Alexander Artyuhov, Erdem Dashinimaev, Darya Avdoshina, Alla Kondrashova, Vladimir Valuev-Elliston, Oleg Latyshev, Olesja Eliseeva, Stefan Petkov, Maxim Abakumov, Laura Hippe, Irina Kholodnyuk, Elizaveta Starodubova, Tatiana Gorodnicheva, Alexander Ivanov, Ilya Gordeychuk, Maria Isaguliants.
  Expression of the Reverse Transcriptase Domain of Telomerase Reverse Transcriptase Induces Lytic Cellular Response in DNA-Immunized Mice and Limits Tumorigenic and Metastatic Potential of Murine Adenocarcinoma 4T1 Cells.
  Vaccines (Basel). 2020 Jun 18;8(2):E318. doi: 10.3390/vaccines8020318
  pmid: 32570805

2019

• Bayurova E, Jansons J, Skrastina D, Smirnova O, Mezale D, Kostyusheva A, Kostyushev D, Petkov S, Podschwadt P, Valuev-Elliston V, Sasinovich S, Korolev S, Warholm P, Latanova A, Starodubova E, Tukhvatulin A, Latyshev O, Selimov R, Metalnikov P, Komarov A, Ivanova O, Gorodnicheva T, Kochetkov S, Gottikh M, Strumfa I, Ivanov A, Gordeychuk I, Isaguliants M.
  HIV-1 Reverse Transcriptase Promotes Tumor Growth and Metastasis Formation via ROS-Dependent Upregulation of Twist.
  Oxid Med Cell Longev. 2019 Dec 2;2019:6016278 doi: 10.1155/2019/6016278. eCollection 2019.
  pmid: 31885806
• Isaeva OI, Sharonov GV, Serebrovskaya EO, Turchaninova MA, Zaretsky AR, Shugay M, Chudakov DM.
  Intratumoral immunoglobulin isotypes predict survival in lung adenocarcinoma subtypes.
  J Immunother Cancer. 2019 Oct 29;7(1):279 doi: 10.1186/s40425-019-0747-1
  pmid: 31665076
• Ignatov KB, Blagodatskikh KA, Shcherbo DS, Kramarova TV, Monakhova YA, Kramarov VM.
  Fragmentation Through Polymerization (FTP): A new method to fragment DNA for next-generation sequencing.
  PLoS One. 2019 Apr 1;14(4):e0210374 doi: 10.1371/journal.pone.0210374. eCollection,2019.
  pmid: 30933980

2018

• Kotlobay AA, Sarkisyan KS, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova LI, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldon T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov FA, Yampolsky IV.
  Genetically encodable bioluminescent system from fungi.
  Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):12728-12732 doi: 10.1073/pnas.1803615115
  pmid: 30478037
• Snezhkina AV, Nyushko KM, Zaretsky AR, Shagin DA, Sadritdinova AF, Fedorova MS, Guvatova ZG, Abramov IS, Pudova EA, Alekseev BY, Dmitriev AA, Kudryavtseva AV
  Transcription Factor SAP30 Is Involved in the Activation of NETO2 Gene Expression in Clear Cell Renal Cell Carcinoma.
  Mol Biol (Mosk). 2018 May-Jun;52(3):451-459 doi: 10.7868/S0026898418030072
  pmid: 29989576

2017

• Rodiger S, Burdukiewicz M, Spiess AN, Blagodatskikh K.
  Enabling reproducible real-time quantitative PCR research: the RDML package.
  Bioinformatics. 2017 Dec 15;33(24):4012-4014 doi: 10.1093/bioinformatics/btx528
  pmid: 28961912
• Blagodatskikh KA, Kramarov VM, Barsova EV, Garkovenko AV, Shcherbo DS, Shelenkov AA, Ustinova VV, Tokarenko MR, Baker SC, Kramarova TV, Ignatov KB.
  Improved DOP-PCR (iDOP-PCR): A robust and simple WGA method for efficient amplification of low copy number genomic DNA.
  PLoS One. 2017 Sep 11;12(9):e0184507 doi: 10.1371/journal.pone.0184507. eCollection 2017.
  pmid: 28892497
• Shagin DA, Turchaninova MA, Shagina IA, Shugay M, Zaretsky AR, Zueva OI, Bolotin DA, Lukyanov S, Chudakov DM.
  Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries.
  BMC Genomics. 2017 Jun 5;18(1):440 doi: 10.1186/s12864-017-3815-2
  pmid: 28583065
• Shagin DA, Shagina IA, Zaretsky AR, Barsova EV, Kelmanson IV, Lukyanov S, Chudakov DM, Shugay M.
  A high-throughput assay for quantitative measurement of PCR errors.
  Sci Rep. 2017 Jun 2;7(1):2718 doi: 10.1038/s41598-017-02727-8
  pmid: 28578414
• Shugay M, Zaretsky AR, Shagin DA, Shagina IA, Volchenkov IA, Shelenkov AA, Lebedin MY, Bagaev DV, Lukyanov S, Chudakov DM.
  MAGERI: Computational pipeline for molecular-barcoded targeted resequencing.
  PLoS Comput Biol. 2017 May 5;13(5):e1005480 doi: 10.1371/journal.pcbi.1005480. eCollection 2017 May.
  pmid: 28475621

2015

• Smetanina NS, Mersiyanova IV, Kurnikova MA, Ovsyannikova GS, Hachatryan LA, Bobrynina VO, Maschan MA, Novichkova GA, Lipton JM, Maschan AA.
  Clinical and genomic heterogeneity of Diamond Blackfan anemia in the Russian Federation.
  Pediatr Blood Cancer. 2015 Sep;62(9):1597-600 doi: 10.1002/pbc.25534
  pmid: 25946618
• Luker KE, Pata P, Shemiakina II, Pereverzeva A, Stacer AC, Shcherbo DS, Pletnev VZ, Skolnaja M, Lukyanov KA, Luker GD, Pata I, Chudakov DM.
  Comparative study reveals better far-red fluorescent protein for whole body imaging.
  Sci Rep. 2015 Jun 2;5:10332 doi: 10.1038/srep10332
  pmid: 26035795

2014

• Ignatov KB, Barsova EV, Fradkov AF, Blagodatskikh KA, Kramarova TV, Kramarov VM.
  A strong strand displacement activity of thermostable DNA polymerase markedly improves the results of DNA amplification.
  Biotechniques. 2014 Aug 1;57(2):81-7 doi: 10.2144/000114198
  pmid: 25109293

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.
  A monomeric red fluorescent protein with low cytotoxicity.
  Nat Commun. 2012 Nov 13;3:1204 doi: 10.1038/ncomms2208
  pmid: 23149748
• 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.
  Mapping of quantitative trait loci controlling lifespan in the short-lived fish Nothobranchius furzeri--a new vertebrate model for age research.
  Aging Cell. 2012 Apr;11(2):252-61 doi: 10.1111/j.1474-9726.2011.00780.x
  pmid: 22221414
• Savitsky AP, Rusanov AL, Zherdeva VV, Gorodnicheva TV, Khrenova MG, Nemukhin AV.
  FLIM-FRET Imaging of Caspase-3 Activity in Live Cells Using Pair of Red Fluorescent Proteins.
  Theranostics. 2012;2(2):215-26 doi: 10.7150/thno.3885
  pmid: 22375160

2011

• Bogdanova EA, Shagina IA, Ianushevich IuG, Vagner LL, Lukyanov SA, Shagin DA.
  Preparation of prokaryotic cDNA for high-throughput transcriptome analysis.
  Bioorg Khim. 2011 Nov-Dec;37(6):854-7 (in Russian)
  pmid: 22497085
• Kurnikova M, Maschan M, Dinova E, Shagina I, Finogenova N, Mamedova E, Polovtseva T, Shagin D, Shcherbina A.
  Four novel ELANE mutations in patients with congenital neutropenia.
  Pediatr Blood Cancer. 2011 Aug;57(2):332-5 doi: 10.1002/pbc.23104
  pmid: 21425445
• Shagina IA, Bogdanova EA, Altshuler IM, Lukyanov SA, Shagin DA.
  Application of the duplex-specific nuclease for fast analysis of single nucleotide polymorphisms and detection of target DNA in complex PCR products.
  Bioorg Khim. 2011 Jul-Aug;37(4):522-9 (in Russian)
  pmid: 22096995
• Serebrovskaya EO, Gorodnicheva TV, Ermakova GV, Solovieva EA, Sharonov GV, Zagaynova EV, Chudakov DM, Lukyanov S, Zaraisky AG, Lukyanov KA.
  Light-induced blockage of cell division with a chromatin-targeted phototoxic fluorescent protein.
  Biochem J. 2011 Apr 1;435(1):65-71 doi: 10.1042/BJ20101217
  pmid: 21214518
• Kurnikova M, Dinova E, Shagina I, Shagin D.
  Alu-mediated recombination in the HAX1 gene as the molecular basis of severe congenital neutropenia.
  Am J Med Genet A. 2011 Mar;155(3):660-1 doi: 10.1002/ajmg.a.33893
  pmid: 21344642

2010

• 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.
  Near-infrared fluorescent proteins.
  Nat Methods. 2010 Oct;7(10):827-9 doi: 10.1038/nmeth.1501
  pmid: 20818379
• Chudakov DM, Matz MV, Lukyanov S, Lukyanov KA.
  Fluorescent proteins and their applications in imaging living cells and tissues.
  Physiol Rev. 2010 Jul;90(3):1103-63 doi: 10.1152/physrev.00038.2009 full text
  pmid: 20664080
• Mamedov IZ, Shagina IA, Kurnikova MA, Novozhilov SN, Shagin DA, Lebedev YB.
  A new set of markers for human identification based on 32 polymorphic Alu insertions.
  Eur J Hum Genet. 2010 Jul;18(7):808-14 doi: 10.1038/ejhg.2010.22
  pmid: 20179741
• Shagina I, Bogdanova E, Mamedov IZ, Lebedev Y, Lukyanov S, Shagin D.
  Normalization of genomic DNA using duplex-specific nuclease.
  Biotechniques. 2010 Jun;48(6):455-9 doi: 10.2144/000113422
  pmid: 20569220
• Bogdanova EA, Shagina I, Barsova EV, Kelmanson I, Shagin DA, Lukyanov SA.
  Normalizing cDNA libraries.
  Curr Protoc Mol Biol. 2010 Apr;Chapter 5:Unit 5.12.1-27 doi: 10.1002/0471142727.mb0512s90
  pmid: 20373503

2009

• Bogdanov AM, Bogdanova EA, Chudakov DM, Gorodnicheva TV, Lukyanov S, Lukyanov KA.
  Cell culture medium affects GFP photostability: a solution.
  Nat Methods. 2009 Dec;6(12):859-60 doi: 10.1038/nmeth1209-859
  pmid: 19935837
• Pletnev S, Gurskaya NG, Pletneva NV, Lukyanov KA, Chudakov DM, Martynov VI, Popov VO, Kovalchuk MV, Wlodawer A, Dauter Z, Pletnev V.
  Structural basis for phototoxicity of the genetically encoded photosensitizer KillerRed.
  J Biol Chem. 2009 Nov 13;284(46):32028-39 doi: 10.1074/jbc.M109.054973
  pmid: 19737938
• 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.
  Individual characterization of stably expanded T cell clones in ankylosing spondylitis patients.
  Autoimmunity. 2009 Sep;42(6):525-36 doi: 10.1080/08916930902960362
  pmid: 19657773
• Yampolsky IV, Balashova TA, Lukyanov KA.
  Synthesis and spectral and chemical properties of the yellow fluorescent protein zFP538 chromophore.
  Biochemistry. 2009 Aug 25;48(33):8077-82 doi: 10.1021/bi900719x
  pmid: 19610669
• Bogdanov AM, Mishin AS, Yampolsky IV, Belousov VV, Chudakov DM, Subach FV, Verkhusha VV, Lukyanov S, Lukyanov KA.
  Green fluorescent proteins are light-induced electron donors.
  Nat Chem Biol. 2009 Apr 26;5(7):459-461 doi: 10.1038/nchembio.174
  pmid: 19396176
• Shcherbo D, Souslova EA, Goedhart J, Chepurnykh TV, Gaintzeva A, Shemiakina II, Gadella TW, Lukyanov S, Chudakov DM.
  Practical and reliable FRET/FLIM pair of fluorescent proteins.
  BMC Biotechnol. 2009 Mar 25;9:24 doi: 10.1186/1472-6750-9-24
  pmid: 19321010
• Shcherbo D, Murphy CS, Ermakova GV, Solovieva EA, Chepurnykh TV, Shcheglov AS, Verkhusha VV, Pletnev VZ, Hazelwood KL, Roche PM, Lukyanov S, Zaraisky AG, Davidson MW, Chudakov DM.
  Far-red fluorescent tags for protein imaging in living tissues.
  Biochem J. 2009 Mar 15;418(3):567-74 doi: 10.1042/BJ20081949
  pmid: 19143658
• Bogdanova EA, Shagina IA, Mudrik E, Ivanov I, Amon P, Vagner LL, Lukyanov SA, Shagin DA.
  DSN depletion is a simple method to remove selected transcripts from cDNA populations.
  Mol Biotechnol. 2009 Mar;41((3)):247-53 doi: 10.1007/s12033-008-9131-y
  pmid: 19127453
• Anisimova VE, Barsova EV, Bogdanova EA, Lukyanov SA, Shcheglov AS.
  Thermolabile duplex-specific nuclease.
  Biotechnol Lett. 2009 Feb;31(2):251-7 doi: 10.1007/s10529-008-9850-y
  pmid: 18810329
• Kurnikova M, Shagina I, Khachatryan L, Schagina O, Maschan M, Shagin D.
  Identification of a novel mutation in DKC1 in dyskeratosis congenita.
  Pediatr Blood Cancer. 2009 Jan;52(1):135-7 doi: 10.1002/pbc.21733
  pmid: 18802941

2008

• Subach OM, Gundorov IS, Yoshimura M, Subach FV, Zhang J, Gruenwald D, Souslova EA, Chudakov DM, Verkhusha VV.
  Conversion of Red Fluorescent Protein into a Bright Blue Probe.
  Chem Biol. 2008 Oct 20;15(10):1116-24 doi: 10.1016/j.chembiol.2008.08.006
  pmid: 18940671
• Anisimova VE, Shcheglov AS, Bogdanova EA, Rebrikov DV, Nekrasov AN, Barsova EV, Shagin DA, Lukyanov SA.
  Is crab duplex-specific nuclease a member of the Serratia family of non-specific nucleases?
  Gene. 2008 Jul 15;418(1-2):41-8 doi: 10.1016/j.gene.2008.04.005
  pmid: 18514436
• Anisimova VE, Rebrikov DV, Shagin DA, Kozhemyako VB, Menzorova NI, Staroverov DB, Ziganshin R, Vagner LL, Rasskazov VA, Lukyanov SA, Shcheglov AS.
  Isolation, characterization and molecular cloning of duplex-specific nuclease from the hepatopancreas of the Kamchatka crab.
  BMC Biochem. 2008 May 21;9:14 doi: 10.1186/1471-2091-9-14
  pmid: 18495036
• Schostak N, Pyatkov K, Zelentsova E, Arkhipova I, Shagin D, Shagina I, Mudrik E, Blintsov A, Clark I, Finnegan DJ, Evgen'ev M.
  Molecular dissection of Penelope transposable element regulatory machinery.
  Nucleic Acids Res. 2008 May;36(8):2522-9 doi: 10.1093/nar/gkm1166
  pmid: 18319284
• Bogdanova EA, Shagin DA, Lukyanov SA.
  Normalization of full-length enriched cDNA.
  Mol Biosyst. 2008 Mar;4(3):205-12 doi: 10.1039/b715110c
  pmid: 18437263
• Markvicheva KN, Bogdanova EA, Staroverov DB, Lukyanov S, Belousov VV.
  Imaging of intracellular hydrogen peroxide production with HyPer upon stimulation of HeLa cells with EGF.
  Methods Mol Biol. 2008;476:79-86
  pmid: 19157010

2007

• Shcherbo D, Merzlyak EM, Chepurnykh TV, Fradkov AF, Ermakova GV, Solovieva EA, Lukyanov KA, Bogdanova EA, Zaraisky AG, Lukyanov S, Chudakov DM.
  Bright far-red fluorescent protein for whole-body imaging.
  Nat Methods. 2007 Sep;4(9):741-6
  pmid: 17721542
• Merzlyak EM, Goedhart J, Shcherbo D, Bulina ME, Shcheglov AS, Fradkov AF, Gaintzeva A, Lukyanov KA, Lukyanov S, Gadella TW, Chudakov DM.
  Bright monomeric red fluorescent protein with an extended fluorescence lifetime.
  Nat Methods. 2007 Jul;4(7):555-7
  pmid: 17572680
• Souslova EA, Belousov VV, Lock J, Stromblad S, Kasparov S, Bolshakov AP, Pinelis VG, Labas YA, Lukyanov S, Mayr LM, Chudakov DM.
  Single fluorescent protein-based Ca²⁺ sensors with increased dynamic range.
  BMC Biotechnol. 2007 Jun 29;7:37
  pmid: 17603870
• Zhang L, Gurskaya NG, Merzlyak EM, Staroverov DB, Mudrik NN, Samarkina ON, Vinokurov LM, Lukyanov S, Lukyanov KA.
  Method for real-time monitoring of protein degradation at the single cell level.
  Biotechniques. 2007 Apr;42(4):446, 448, 450
  pmid: 17489230
• Chudakov DM, Lukyanov S, Lukyanov KA.
  Tracking intracellular protein movements using photoswitchable fluorescent proteins PS-CFP2 and Dendra2.
  Nat Protoc. 2007;2(8):2024-32
  pmid: 17703215

2006

• Belousov VV, Fradkov AF, Lukyanov KA, Staroverov DB, Shakhbazov KS, Terskikh AV, Lukyanov S.
  Genetically encoded fluorescent indicator for intracellular hydrogen peroxide.
  Nat Methods. 2006 Apr;3(4):281-6
  pmid: 16554833
• Gurskaya NG, Verkhusha VV, Shcheglov AS, Staroverov DB, Chepurnykh TV, Fradkov AF, Lukyanov S, Lukyanov KA.
  Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light.
  Nat Biotechnol. 2006 Apr;24(4):461-5
  pmid: 16550175
• Bulina ME, Chudakov DM, Britanova OV, Yanushevich YG, Staroverov DB, Chepurnykh TV, Merzlyak EM, Shkrob MA, Lukyanov S, Lukyanov KA.
  A genetically encoded photosensitizer.
  Nat Biotechnol. 2006 Jan;24(1):95-9
  pmid: 16369538
• Bulina ME, Lukyanov KA, Britanova OV, Onichtchouk D, Lukyanov S, Chudakov DM.
  Chromophore-assisted light inactivation (CALI) using the phototoxic fluorescent protein KillerRed.
  Nat Protoc. 2006;1(2):947-53
  pmid: 17406328

2005

• Chudakov DM, Lukyanov S, Lukyanov KA.
  Fluorescent proteins as a toolkit for in vivo imaging.
  Trends Biotechnol. 2005 Dec;23(12):605-13
  pmid: 16269193