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Научные публикации

Публикации в научных журналах с участием сотрудников NOVEL
2022
Christopher Lance, Malte D. Luecken, Daniel B. Burkhardt, Robrecht Cannoodt, Pia Rautenstrauch, Anna Laddach, Aidyn Ubingazhibov, Zhi-Jie Cao, Kaiwen Deng, Sumeer Khan, Qiao Liu, Nikolay Russkikh, Gleb Ryazantsev, Uwe Ohler, NeurIPS 2021 Multimodal data integration competition participants, Angela Oliveira Pisco, Jonathan Bloom, Smita Krishnaswamy, Fabian J. Theis
2021
Bennett J, Pomaznoy M, Singhania A, Peters B.
PLoS Comput Biol. 2021;17: e1009459. doi:10.1371/journal.pcbi.1009459
da Silva Antunes R, Soldevila F, Pomaznoy M, Babor M, Bennett J, Tian Y, et al.
JCI Insight. 2021;6. doi:10.1172/jci.insight.141023
Tippalagama R, Singhania A, Dubelko P, Lindestam Arlehamn CS, Crinklaw A, Pomaznoy M, et al.
JI. 2021;207: 523–533. doi:10.4049/jimmunol.2100011
Generation of an induced pluripotent stem cell line, ICGi028-A, by reprogramming peripheral blood mononuclear cells of a patient suffering from hypertrophic cardiomyopathy and carrying a heterozygous p.E510Q mutation in HADHA
Dementyeva EV, Vyatkin YV, Chernyavsky AM, Zakian SM.
Stem Cell Res. 2021 May;53:102348. doi: 10.1016/j.scr.2021.102348. Epub 2021 Apr 19. PMID: 33887580
Cao H, Xu D, Cai Y, Han X, Tang L, Gao F, Qi Y, Cai D, Wang H, Ri M, Antonets D, Vyatkin Y, Chen Y, You X, Wang F, Nicolas E, Kapranov P.
BMC Biol. 2021 May 20;19(1):108. doi: 10.1186/s12915-021-01044-x. PMID: 34016118; PMCID: PMC8139166
Ufuk Ergun, Bahar Say, Sezen Guntekin Ergun, Ferda Emriye Percin, Levent Inan, Sukran Kaygisiz, Pınar Gelener Asal, Buket Yurteri, Maksim Struchalin, Dmitry Shtokalo, Mehmet Ali Ergun.
European Journal of Medical Genetics. V64(4), April 2021
St Laurent G 3rd, Toma I, Seilheimer B, Cesnulevicius K, Schultz M, Tackett M, Zhou J, Ri M, Shtokalo D, Antonets D, Jepson T, McCaffrey TA.
BMC Genomics. 2021 Nov 25;22(1):854. doi: 10.1186/s12864-021-08083-2.
McCaffrey, T.A., Toma, I., Yang, Z., Katz, R., Reiner, J., Mazhari, R., Shah, P., Tackett, M., Jones, D., Jepson, T., Falk, Z., Wargodsky, R., Shtakalo, D., Antonets, D., Ertle, J., Kim, J., Lai, Y., Arslan, Z., Aledort, E., Alfaraidy M., St.Laurent III, G.
BMC Med Genomics 14, 216 (2021)
2020
Burel JG, Pomaznoy M, Lindestam Arlehamn CS, Seumois G, Vijayanand P, Sette A, et al.
Cytometry A. 2020;97: 1127–1135. doi:10.1002/cyto.a.24027
Pomaznoy M, Kuan R, Lindvall M, Burel JG, Seumois G, Vijayanand P, et al.
Immunohorizons. 2020;4: 292–307. doi:10.4049/immunohorizons.2000031
Bazhan S, Antonets D, Starostina E, Ilyicheva T, Kaplina O, Marchenko V, Durymanov A, Oreshkova S, Karpenko L
Vaccines (Basel). 2020 Aug 9;8(3):448. doi: 10.3390/vaccines8030448. PMID: 32784907; PMCID: PMC7565880.
In silico design of influenza a virus artificial epitope-based T-cell antigens and the evaluation of their immunogenicity in mice
Bazhan SI, Antonets DV, Starostina EV, Ilyicheva TN, Kaplina ON, Marchenko VY, Volkova OY, Bakulina AY, Karpenko LI
J Biomol Struct Dyn. 2022 Apr;40(7):3196-3212. doi: 10.1080/07391102.2020.1845978. Epub 2020 Nov 23. PMID: 33222632.
Karpenko LI, Apartsin EK, Dudko SG, Starostina EV, Kaplina ON, Antonets DV, Volosnikova EA, Zaitsev BN, Bakulina AY, Venyaminova AG, Ilyichev AA, Bazhan SI.
Vaccines (Basel). 2020 Dec 1;8(4):718. doi: 10.3390/vaccines8040718. PMID: 33271964; PMCID: PMC7760684.
Methods of editing of genes and genomes
Abbat A.V., …, Vyatkin Y.V., …, Yurlova E.V.
SB RAS, 2020 (in Russian)
Generation of two clonal iPSC lines, ICGi019-A and ICGi019-B, by reprogramming peripheral blood mononuclear cells of a patient suffering from hypertrophic cardiomyopathy and carrying a heterozygous p.M659I mutation in MYH7
Dementyeva EV, Kovalenko VR, Zhiven MK, Ustyantseva EI, Kretov EI, Vyatkin YV, Zakian SM.
Stem Cell Res. 2020 Jul;46:101840. doi: 10.1016/j.scr.2020.101840. Epub 2020 May 11. PMID: 32422568
Generation of three Duchenne muscular dystrophy patient-derived induced pluripotent stem cell (iPSC) lines ICGi002-A, ICGi002-B and ICGi002-C
Valetdinova KR, Maretina MA, Vyatkin YV, Perepelkina MP, Egorova AA, Baranov VS, Kiselev AV, Gershovich PM, Zakian SM.
Stem Cell Res. 2020 Oct;48:101941. doi: 10.1016/j.scr.2020.101941. Epub 2020 Aug 3. PMID: 32777771
Generation of induced pluripotent stem cell lines ICGi021-A and ICGi022-A from peripheral blood mononuclear cells of two healthy individuals from Siberian population
Malakhova AA, Grigor'eva EV, Pavlova SV, Malankhanova TB, Valetdinova KR, Vyatkin YV, Khabarova EA, Rzaev JA, Zakian SM, Medvedev SP.
Stem Cell Res. 2020 Oct;48:101952. doi: 10.1016/j.scr.2020.101952. Epub 2020 Aug 8. PMID: 32805537
Study of the effect of the introduction of mitochondrial import determinants into the gRNA structure on the activity of the gRNA/SpCas9 complex in vitro
Zakirova EG, Vyatkin YV, Verechshagina NA, Muzyka VV, Mazunin IO, Orishchenko KE.
Vavilovskii Zhurnal Genet Selektsii. 2020 Aug;24(5):512-518. doi: 10.18699/VJ20.643. PMID: 33659835; PMCID: PMC7716540
Мутации в генах ARID1A и SMARCA4 при рецидивах диффузной в-крупноклеточной лимфомы с поражением ЦНС
Воропаева Е.Н., Поспелова Т.И., Максимов В.Н., Березина О.В., Карпова В.С., Рзаев Д.А., Колесникова М.А., Вяткин Ю.В., Штокало Д.Н., Баширзаде К.А., Иванова А.А., Мельникова Е.С., Гуражева А.А.
Медицинская генетика. 2020. Т. 19. № 6 (215). С. 90-92.
McCaffrey TA, St Laurent G 3rd, Shtokalo D, Antonets D, Vyatkin Y, Jones D, Battison E, Nigg JT.
BMC Med Genomics. 2020 Oct 28;13(1):160. doi: 10.1186/s12920-020-00808-8. PMID: 33115496; PMCID: PMC7594430.
Disease Pathways: An Atlas of Human Disease Signaling Pathways.
AP. Nesterova, EA. Klimov, M. Zharkova, S. Sozin, V. Sobolev, NV. Ivanikova, M. Shkrob, and A. Yuryev.
Amsterdam (The Netherlands) and New York: Elsevier. ISBN: 978-0-12-817086-1. 2020
Denis Antonets, Nikolai Russkikh, Antoine Sanchez, Victoria Kovalenko, Elvira Bairamova, Dmitry Shtokalo, Sergey Medvedev, Suren Zakian
Sensors (Basel). 2020 Jun 29;20(13):3653. doi: 10.3390/s20133653.
Nikolai Russkikh, Denis Antonets, Dmitry Shtokalo, Alexander Makarov, Yuri Vyatkin, Alexey Zakharov, Evgeny Terentyev
Bioinformatics, Volume 36, Issue 20, 15 October 2020
2019
Burel JG, Babor M, Pomaznoy M, Lindestam Arlehamn CS, Khan N, Sette A, et al.
Front Immunol. 2019;10: 221. doi:10.3389/fimmu.2019.00221
Burel JG, Pomaznoy M, Lindestam Arlehamn CS, Weiskopf D, da Silva Antunes R, Jung Y, et al.
Elife. 2019;8. doi:10.7554/eLife.46045
Pomaznoy M, Sethi A, Greenbaum J, Peters B.
Sci Rep. 2019;9: 16342. doi:10.1038/s41598-019-52584-w
Rudometov AP, Chikaev AN, Rudometova NB, Antonets DV, Lomzov AA, Kaplina ON, Ilyichev AA, Karpenko LI
Vaccines (Basel). 2019 Aug 6;7(3):83. doi: 10.3390/vaccines7030083. PMID: 31390770; PMCID: PMC6789618.
Sharipova DV, Kovalenko VR, Bairamova EM, Vartanova VA, Grigor'eva EV, Vyatkin YV, Khabarova EA, Rzaev DA, Zakian SM, Medvedev SP.
Stem Cell Res. 2019 Dec;41:101652. doi: 10.1016/j.scr.2019.101652. Epub 2019 Nov 9. PMID: 31733442
Dementyeva EV, Medvedev SP, Kovalenko VR, Vyatkin YV, Kretov EI, Slotvitsky MM, Shtokalo DN, Pokushalov EA, Zakian SM.
Biochemistry (Mosc). 2019 Mar; 84(3):291-298. doi:10.1134/S0006297919030118
Sherstyuk VV, Davletshina GI, Vyatkin YV, Shtokalo DN, Vlasov VV, Zakian SM.
Acta Naturae. 2019 Apr-Jun;11(2):92-97. doi: 10.32607/20758251-2019-11-2-92-97
2018
Pomaznoy M, Ha B, Peters B.
BMC Bioinformatics. 2018;19: 470. doi:10.1186/s12859-018-2533-3
Ovchinnikov VY, Antonets DV, Gulyaeva LF
J Bioinform Comput Biol. 2018 Feb;16(1):1750029. doi: 10.1142/S0219720017500299. Epub 2017 Dec 10. PMID: 29301444.
Borobova EA, Antonets DV, Starostina EV, Karpenko LI, Ilyichev AA, Bazhan SI.
Curr Gene Ther. 2018;18(6):375-385. doi: 10.2174/1566523218666181113112829. PMID: 30421674.
Diao Y, Rahman MF, Vyatkin Y, Azatyan A, St Laurent G, Kapranov P, Zaphiropoulos PG.
Mol Oncol. 2018 Oct;12(10):1718-1734. doi: 10.1002/1878-0261.12366. Epub 2018 Aug 30. PMID: 30098229; PMCID: PMC6166001
Sherstyuk V.V., Medvedev S.P., Ri M.T., Vyatkin Y.V., Saik O.V., Shtokalo D.N., Zakian S.M.
Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2018;22(2):179-186. DOI 10.18699/VJ18.345
Anisimenko M.S., Paul G.A., Kozyakov A.E., Gutkina N.I., Berdyugina D.A., Garanin A.Y., Butorina A.V., Gornostaeva E.V., Khafizov K.F., Vyatkin Y.V., Shtokalo D.N., Kovalenko S.P.
Siberian journal of oncology. 2018;17(4):53-58.
St. Laurent G, Toma I, Seilheimer B, Tackett M, Zhou J, Ri M, Shtokalo D, Vyatkin Y, Jepson T, Cesnulevicius K, McCaffrey T.
Annals of the Rheumatic Diseases 2018;77:238-239
2017
St. Laurent G III, Seilheimer B, Tackett M, Zhou J, Shtokalo D, Vyatkin Y, Ri M, Toma I, Jones D and McCaffrey TA.
Front. Mol. Biosci. 4:57. 2017. doi: 10.3389/fmolb.2017.00057.
G.St Laurent III, B. Seilheimer, M. Tackett, J. Zhou, D. Shtokalo, Y. Vyatkin, P. Kapranov, I. Toma, T. Mccaffrey.
Annals of the Rheumatic Diseases. V.76. P.202. June 2017. DOI: 10.1136/annrheumdis-2017-eular.4964
Metagenomic analysis in Lake Onego (Russia) Synechococcus cyanobacteria.
A. Vasileva, M. Skopina, S. Averina, O. Gavrilova, N. Ivanikova, A. Pinevich.
Journal of Great Lakes Research. 2017
Chernyi, V. S., Tarasova, P. V., Kozlov, V. V., Saik, O. V., Kushlinskii, N. E., & Gulyaeva, L. F.
Bulletin of experimental biology and medicine, 163(5), 655-659. DOI: 10.1007/s10517-017-3872-1
V.Sherstyuk, S.Medvedev, E.Elisaphenko, E.Vaskova, M.Ri, Y.Vyatkin, O.Saik, D.Shtokalo, E.Pokushalov, S.Zakian.
Scientific reports. 2017 Jun 5;7(1):2787. doi: 10.1038/s41598-017-02632-0
2016
G. St. Laurent, Y. Vyatkin, D. Antonets, M. Ri, Y. Qi, O. Saik, D. Shtokalo, M. J.L. de Hoon, H. Kawaji, M. Itoh, T. Lassmann, E. Arner, A.R.R. Forrest, The FANTOM consortium, E. Nicolas, T.A. McCaffrey, P. Carninci, Y. Hayashizaki, C. Wahlestedt, and P. Kapranov.
Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw162
2014
St Laurent G, Vyatkin Y, Kapranov P.
BMC Med. 2014 Jun 12;12(1):97. doi: 10.1186/1741-7015-12-97.
2013
St Laurent G, Tackett MR, Nechkin S, Shtokalo D, Antonets D, Savva YA, Maloney R, Kapranov P, Lawrence CE, Reenan RA
Nature Structural and Molecular Biology. 2013 Sep 29. doi: 10.1038/nsmb.2675
Georges St Laurent, Dmitry Shtokalo, Biao Dong, Michael R Tackett, Xiaoxuan Fan, Sandra Lazorthes, Estelle Nicolas, Nianli Sang, Timothy J Triche, Timothy A McCaffrey, Weidong Xiao and Philipp Kapranov
Genome Biology. 2013 July 22, 14:R73. doi:10.1186/gb-2013-14-7-r73
St Laurent G, Shtokalo D, Tackett MR, Yang Z, Vyatkin Y, Milos PM, Seilheimer B, McCaffrey TA, Kapranov P
Methods. 2013 Apr 4. pii: S1046-2023(13)00096-0. doi: 10.1016/j.ymeth.2013.03.027.
2012
On limiting transition in the model of multistage multiphase synthesis of substance
Shtokalo D.
Siberian Journal of Industrial Math. 15:4 (2012), p. 135–146 (in Russian)
St Laurent G 3rd, Shtokalo D, Heydarian M, Palyanov A, Babiy D, Zhou J, Kumar A, Urcuqui-Inchima S
Molecular Genetics and Genomics. 2012 Dec; 287(11-12):867-79. doi: 10.1007/s00438-012-0722-8
Georges St Laurent, Dmitry Shtokalo, Michael R Tackett, Zhaoqing Yang, Tatyana Eremina, Claes Wahlestedt, Silvio Urcuqui-Inchima, Bernd Seilheimer, Timothy A McCaffrey and Philipp Kapranov
BMC Genomics. 2012 Sep 24;13:504. doi: 10.1186/1471-2164-13-504
Andrey Palyanov, Sergey Khayrulin, Stephen D. Larson, and Alexander Dibert.
In Silico Biology. 2011-2012; 11(3-4):137-47. doi: 10.3233/ISB-2012-0445
2011
Development of integrated environment for miRNA search and analysis
Nechkin S., Shtokalo D., Palyanov A., Sheremushkin E.
Intelligent software. PSI-2011, p. 176-179 (in Russian)
2010
Structural analysis of RNA sequences interacted with HuR protein
Palyanov A., Sheremushkin E., Shtokalo D., Nechkin S., Heydarian M., G.St.Laurent
Software products and systems, 2010, No.3 (in Russian)
2009
On limiting transition to delayed equation in the model of synthesis of substance with reversibility and sinks
Shtokalo D.
Siberian Journal of Industrial Math. 12:2 (2009), p.143-156 (in Russian).
2008
The integrated environment for miRNA search and analysis
Nechkin S., Palyanov A., Cheremushkin E., Shtokalo D., Albert P., St.Laurent G.
Software products and systems, 2008, No.4, p.151-153 (in Russian)
2007
Study of a model of linear biomolecular synthesis with reversible processes
Fadeev S., Likhoshvai V., Shtokalo D.
J. Appl. Indust. Math., 2007, v.1(2), p.178-189
2006
Transformation of cycles based on non-singular matrices
Osmonov R., Shtokalo D.
Problems of intellectualization and quality of informatics systems, “Construction and optimization of programs”. Novosibirsk, 2006, p.162-176 (in Russian).
Waleev T, Shtokalo D, Konovalova T, Voss N, Cheremushkin E, Stegmaier P, Kel-Margoulis O, Wingender E, Kel A.
Nucleic Acids Research. 2006 Jul 1;34(Web Server issue):W541-5
2003
Kel, A., Gössling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O., Wingender, E.
Nucleic acids research. 31. 3576-3579. 10.1093/nar/gkg585.