Штокало Дмитрий Николаевич

Штокало Дмитрий Николаевич
Должность
Директор
Ученая степень
Кандидат физико-математических наук
в команде Novel
с 2004 года
Образование
Высшее, механико-математический факультет НГУ,
Экономический факультет НГУ
Проекты
Genomenal NGS Wizard, Генокарта, SLI Environment, ExPlain, обработка NGS RNAseq, microarrays
Интересы
Биоинформатика, математика в биологии, развитие компании

Ссылки

ResearchGate
LinkedIn

Список публикаций

2023
RNAseq profiling of blood from patients with coronary artery disease: Signature of a T cell imbalance
Timothy A. McCaffrey, Ian Toma, Zhaoqing Yang, Richard Katz, Jonathan Reiner, Ramesh Mazhari, Palak Shah, Zachary Falk, Richard Wargowsky, Jennifer Goldman, Dan Jones, Dmitry Shtokalo, Denis Antonets, Tisha Jepson, Anastasia Fetisova, Kevin Jaatinen, Natalia Ree, Maxim Ri
Transcriptomic Analysis of CRISPR/Cas9-Mediated PARP1-Knockout Cells under the Influence of Topotecan and TDP1 Inhibitor
Nadezhda S. Dyrkheeva, Anastasia A. Malakhova, Aleksandra L. Zakharenko, Larisa S. Okorokova,Dmitriy N. Shtokalo, Sophia V. Pavlova, Sergey P. Medvedev, Suren M. Zakian, Anna A. Nushtaeva, Alexey E. Tupikin , Marsel R. Kabilov, Svetlana N. Khodyreva , Olga A. Luzina, Nariman F. Salakhutdinov and Olga I. Lavrik
2021
Genome-wide association and whole exome sequencing studies reveal a novel candidate locus for restless legs syndrome
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
RNAseq analysis of treatment-dependent signaling changes during inflammation in a mouse cutaneous wound healing model
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.
RNA sequencing of blood in coronary artery disease: involvement of regulatory T cell imbalance
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
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.
CellCountCV-A Web-Application for Accurate Cell Counting and Automated Batch Processing of Microscopic Images Using Fully Convolutional Neural Networks
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.
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
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
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
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.
VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer
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
Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila
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
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)
Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells
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
Insights from the HuR-interacting transcriptome: ncRNAs, ubiquitin pathways, and patterns of secondary structure dependent RNA interactions
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
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).
Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm
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
Штокало Дмитрий Николаевич

Ссылки

ResearchGate
LinkedIn

Штокало Дмитрий Николаевич

Должность
Директор
Ученая степень
Кандидат физико-математических наук
в команде Novel
с 2004 года
Образование
Высшее, механико-математический факультет НГУ,
Экономический факультет НГУ
Проекты
Genomenal NGS Wizard, Генокарта, SLI Environment, ExPlain, обработка NGS RNAseq, microarrays
Интересы
Биоинформатика, математика в биологии, развитие компании

Список публикаций

2023
RNAseq profiling of blood from patients with coronary artery disease: Signature of a T cell imbalance
Timothy A. McCaffrey, Ian Toma, Zhaoqing Yang, Richard Katz, Jonathan Reiner, Ramesh Mazhari, Palak Shah, Zachary Falk, Richard Wargowsky, Jennifer Goldman, Dan Jones, Dmitry Shtokalo, Denis Antonets, Tisha Jepson, Anastasia Fetisova, Kevin Jaatinen, Natalia Ree, Maxim Ri
Transcriptomic Analysis of CRISPR/Cas9-Mediated PARP1-Knockout Cells under the Influence of Topotecan and TDP1 Inhibitor
Nadezhda S. Dyrkheeva, Anastasia A. Malakhova, Aleksandra L. Zakharenko, Larisa S. Okorokova,Dmitriy N. Shtokalo, Sophia V. Pavlova, Sergey P. Medvedev, Suren M. Zakian, Anna A. Nushtaeva, Alexey E. Tupikin , Marsel R. Kabilov, Svetlana N. Khodyreva , Olga A. Luzina, Nariman F. Salakhutdinov and Olga I. Lavrik
2021
Genome-wide association and whole exome sequencing studies reveal a novel candidate locus for restless legs syndrome
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
RNAseq analysis of treatment-dependent signaling changes during inflammation in a mouse cutaneous wound healing model
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.
RNA sequencing of blood in coronary artery disease: involvement of regulatory T cell imbalance
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
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.
CellCountCV-A Web-Application for Accurate Cell Counting and Automated Batch Processing of Microscopic Images Using Fully Convolutional Neural Networks
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.
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
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
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
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.
VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer
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
Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila
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
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)
Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells
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
Insights from the HuR-interacting transcriptome: ncRNAs, ubiquitin pathways, and patterns of secondary structure dependent RNA interactions
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
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).
Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm
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