Dmitrii Smirnov

Research advisors: Ekaterina Khrameeva, Debra Toiber

Program entry year: 2019

Graduated from Moscow Institute of Physics and Technology, in 2019

Research project: Investigation of the role of SIRT6 in molecular mechanisms of gene expression regulation, metabolism and aging

Research interests: Bioinformatics, sirtuins, aging, chromatin interactions, metabolomics

Publications:

• Smirnov D, Pikunov A, Syunyaev R, Deviatiiarov R, Gusev O, Aras K, et al. (2020) “Genetic algorithm-based personalized models of human cardiac action potential“. PLoS ONE 15(5): e0231695. https://doi.org/10.1371/journal.pone.0231695
• Mazor G, Smirnov D, Ben David H, Khrameeva E, Toiber D, Rotblat B. (2021) “TP73-AS1 is induced by YY1 during TMZ treatment and highly expressed in the aging brain”. Aging (Albany NY).; 13:14843-14861. https://doi.org/10.18632/aging.203182
• Smirnov, D.; Mazin, P.; Osetrova, M.; Stekolshchikova, E.; Khrameeva, E. (2021). “The Hitchhiker’s Guide to Untargeted Lipidomics Analysis: Practical Guidelines”. Metabolites, 11, 713. https://doi.org/10.3390/metabo11110713
• Stekolshchikova, E. A., Tkachev, A. I., Osetrova, M. S., Smirnov, D. N., Efimova, O. I., & Khrameeva, E. E. (2021). “Application of mass spectrometry methods to the analysis of lipid composition of the human brain”. Biotekhnologiya, 37(5), 80-87. https://doi.org/10.21519/0234-2758-2021-37-5-80-87
• Smirnov, D. N., Shekhovtsov, S. V., Shipova, A. A., Gazizova, G. R., Shagimardanova, E. I., Bulakhova, N. A., Meshcheryakova, E. N., Poluboyarova, T. V., Khrameeva, E. E., Peltek, S. E., & Berman, D. I. (2022). “De novo assembly and analysis of the transcriptome of the Siberian wood frog Rana amurensis”. Vavilovskii zhurnal genetiki i selektsii, 26(1), 109–116. https://doi.org/10.18699/VJGB-22-07

Conference presentations:

• Smirnov DN, Khrameeva EE “Topologically Associating Domain optimal set prediction using Armatus software” – Oral presentation at ITASb, online conference, April 2020
• Dmitrii Smirnov, Ekaterina Khrameeva, “optimalTAD: a novel algorithm for Topologically Associating Domain optimal set prediction” – poster presentation at Moscow Conference on Computational Molecular Biology (MCCMB’21)
• Dmitrii Smirnov, Ekaterina Eremenko, Daniel Stein, Shai Kaluski, Weronika Jasinska, Ekaterina Khrameeva, Debra Toiber, “The role of SIRT6 in the regulation of mitochondrial functions” – poster presentation at Aging and Epigenetics meeting-II, Ramat Gan, Israel.
• D Smirnov, E Eremenko, D Stein, S Kaluski, W Jasinska, E Khrameeva, D Toiber. “The emerging role of SIRT6 in the mitochondrial regulation” – poster presentation at Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022), Novosibirsk, Russia.

Grants:

• 21-74-20050 – RSF – “Mechanisms of the Siberian frog (Rana amurensis) resistance to anoxia”  (2021 – 2024)
• 21-34-70051 – mol_a_mos – “Development of algorithms for analyzing Hi-C data of DNA packaging within cell nuclei” (2021 – 2023)
• Skoltech students core facility grant (autumn 2020) – A novel approach discovering optimal TAD annotation
• Skoltech students core facility grant (summer 2022) – A novel approach discovering optimal TAD annotation (continuation of the project)