Vyatkin Yuri Viktorovich

Vyatkin Yuri Viktorovich
Post
Chief Innovation Officer
in the Novel team
since 2010
Education
NSU, master (Applied Mathematics and Informatics (2006) and Philosophy (2008)), graduate school (Bioinformatics, 2009),
Universite de Lausanne (UNIL/EPFL), Switzerland (2009),
Brown University, USA (2010),
University of Trento, Italy (2018)
Projects
NGS Wizard, Protomenal
Interests
Bioinformatics, Medical genetics, Pharmacogenetics, Genetic engineering, Genome editing, Human and animal genomics, Prokaryotic genomics, Genome assembly, Proteomics, Structural bioinformatics, Molecular dynamics calculations, Transcriptomics, Modern DNA and RNA sequencing platforms, Mass spectrometric analysis, Metagenomics, Molecular Biology, Biochemistry, Genetics, Systemic Bioinformatics, Phylogenetic Analysis, Computational Biology, Algorithmic Bioinformatics, Data Mining, Data Science, Big Data, Bioinformatics Machine Learning, Biomedical Artificial Intelligence, High Performance Computing, Supercomputing, DevOps, DataOps, Biomedical Data Processing Platforms, Biomedical Software Development, Biomedical Project Management, Biomedical Industry Trends

List of publications

2023
The Metagenomic Analysis of Viral Diversity in Colorado Potato Beetle Public NGS Data
Maria Starchevskaya, Ekaterina Kamanova, Yuri Vyatkin, Tatyana Tregubchak, Tatyana Bauer, Sergei Bodnev, Ulyana Rotskaya, Olga Polenogova, Vadim Kryukov and Denis Antonets
2021
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
Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans
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
2020
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.
Biomarker discovery in attention deficit hyperactivity disorder: RNA sequencing of whole blood in discordant twin and case-controlled cohorts
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.
Style transfer with variational autoencoders is a promising approach to RNA-Seq data harmonization and analysis
Nikolai Russkikh, Denis Antonets, Dmitry Shtokalo, Alexander Makarov, Yuri Vyatkin, Alexey Zakharov, Evgeny Terentyev
Bioinformatics, Volume 36, Issue 20, 15 October 2020
2019
Generation of two iPSC lines, (ICGi015-A and ICGi015-B), by reprogramming peripheral blood mononuclear cells from a patient with Parkinson's disease
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
Applying Patient-Specific Induced Pluripotent Stem Cells to Create a Model of Hypertrophic Cardiomyopathy
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
A New MicroRNA Cluster Involved in the Reprogramming to a Pluripotent State
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
Identification of novel GLI1 target genes and regulatory circuits in human cancer cells
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
The search for microRNAs potentially involved in the self-renewal maintaining of laboratory rat pluripotent stem cells
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
The spectrum of BRCA1 gene mutations in early onset breast cancer patients from Russia
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.
THU0021 Differential effects of tr14 versus diclofenac on cox/lox pathways revealed by RNASeq
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
Genome-wide profiling and differential expression of microRNA in rat pluripotent stem cells
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
Deep Sequencing Transcriptome Analysis of Murine Wound Healing: Effects of a Multicomponent, Multitarget Natural Product Therapy-Tr14.
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.
Deep sequencing transcriptome analysis of the effect of traumeel versus diclofenac therapeutic action in wound healing
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
2016
Functional annotation of the vlinc class of non-coding RNAs using systems biology approach
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
Dark matter RNA illuminates the puzzle of genome-wide association studies
St Laurent G, Vyatkin Y, Kapranov P.
BMC Med. 2014 Jun 12;12(1):97. doi: 10.1186/1741-7015-12-97.
2013
On the importance of small changes in RNA expression
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.

Teaching

2021–2022
Department of Information Technologies NSU

 

Bioinformatics (two-semester course)

NSMU

Introduction to modern genetic diagnostics

 

2020–2021
Department of Natural Sciences NSU

General bioinformatics (two-semester course)

2019–2020
Department of Natural Sciences NSU

General bioinformatics (two-semester course)

Vyatkin Yuri Viktorovich

Vyatkin Yuri Viktorovich

Post
Chief Innovation Officer
in the Novel team
since 2010
Education
NSU, master (Applied Mathematics and Informatics (2006) and Philosophy (2008)), graduate school (Bioinformatics, 2009),
Universite de Lausanne (UNIL/EPFL), Switzerland (2009),
Brown University, USA (2010),
University of Trento, Italy (2018)
Projects
NGS Wizard, Protomenal
Interests
Bioinformatics, Medical genetics, Pharmacogenetics, Genetic engineering, Genome editing, Human and animal genomics, Prokaryotic genomics, Genome assembly, Proteomics, Structural bioinformatics, Molecular dynamics calculations, Transcriptomics, Modern DNA and RNA sequencing platforms, Mass spectrometric analysis, Metagenomics, Molecular Biology, Biochemistry, Genetics, Systemic Bioinformatics, Phylogenetic Analysis, Computational Biology, Algorithmic Bioinformatics, Data Mining, Data Science, Big Data, Bioinformatics Machine Learning, Biomedical Artificial Intelligence, High Performance Computing, Supercomputing, DevOps, DataOps, Biomedical Data Processing Platforms, Biomedical Software Development, Biomedical Project Management, Biomedical Industry Trends

List of publications

2023
The Metagenomic Analysis of Viral Diversity in Colorado Potato Beetle Public NGS Data
Maria Starchevskaya, Ekaterina Kamanova, Yuri Vyatkin, Tatyana Tregubchak, Tatyana Bauer, Sergei Bodnev, Ulyana Rotskaya, Olga Polenogova, Vadim Kryukov and Denis Antonets
2021
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
Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans
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
2020
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.
Biomarker discovery in attention deficit hyperactivity disorder: RNA sequencing of whole blood in discordant twin and case-controlled cohorts
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.
Style transfer with variational autoencoders is a promising approach to RNA-Seq data harmonization and analysis
Nikolai Russkikh, Denis Antonets, Dmitry Shtokalo, Alexander Makarov, Yuri Vyatkin, Alexey Zakharov, Evgeny Terentyev
Bioinformatics, Volume 36, Issue 20, 15 October 2020
2019
Generation of two iPSC lines, (ICGi015-A and ICGi015-B), by reprogramming peripheral blood mononuclear cells from a patient with Parkinson's disease
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
Applying Patient-Specific Induced Pluripotent Stem Cells to Create a Model of Hypertrophic Cardiomyopathy
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
A New MicroRNA Cluster Involved in the Reprogramming to a Pluripotent State
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
Identification of novel GLI1 target genes and regulatory circuits in human cancer cells
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
The search for microRNAs potentially involved in the self-renewal maintaining of laboratory rat pluripotent stem cells
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
The spectrum of BRCA1 gene mutations in early onset breast cancer patients from Russia
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.
THU0021 Differential effects of tr14 versus diclofenac on cox/lox pathways revealed by RNASeq
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
Genome-wide profiling and differential expression of microRNA in rat pluripotent stem cells
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
Deep Sequencing Transcriptome Analysis of Murine Wound Healing: Effects of a Multicomponent, Multitarget Natural Product Therapy-Tr14.
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.
Deep sequencing transcriptome analysis of the effect of traumeel versus diclofenac therapeutic action in wound healing
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
2016
Functional annotation of the vlinc class of non-coding RNAs using systems biology approach
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
Dark matter RNA illuminates the puzzle of genome-wide association studies
St Laurent G, Vyatkin Y, Kapranov P.
BMC Med. 2014 Jun 12;12(1):97. doi: 10.1186/1741-7015-12-97.
2013
On the importance of small changes in RNA expression
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.

Teaching

2021–2022
Department of Information Technologies NSU

 

Bioinformatics (two-semester course)

NSMU

Introduction to modern genetic diagnostics

 

2020–2021
Department of Natural Sciences NSU

General bioinformatics (two-semester course)

2019–2020
Department of Natural Sciences NSU

General bioinformatics (two-semester course)