CV

Education

• B.S. in Applied Mathematics and Physics, Moscow Institute of Physics and Technology, 2013-2017
• M.S. in Applied Mathematics and Physics, Moscow Institute of Physics and Technology, 2017-2019
• Ph.D in Life Sciences, Dual-degree program between Skolkovo Institute of Science and Technology (Russia) and Ben-Gurion University of the Negev (Israel), 2019-2023

Research experience

• 2024 - Present: Research Scientist
  • Khrameeva Lab (Skoltech, Moscow, Russia)
  • Supervisor: Prof. Ekaterina Khrameeva
  • Research interests: Bioinformatics, computational biology, sirtuins, aging, chromatin interactions, metabolomics
• 2023 - 2024: Junior Research Scientist
  • Khrameeva Lab (Skoltech, Moscow, Russia)
  • Supervisor: Prof. Ekaterina Khrameeva
• 2019 - 2023: Ph.D student
  • Khrameeva Lab (Skoltech, Moscow, Russia) and Toiber Lab (BGU, Beer Sheba, Israel)
  • Thesis: Investigation of the role of SIRT6 in molecular mechanisms of gene expression, metabolism regulation and aging
  • Supervisor: Prof. Ekaterina Khrameeva and Prof Debra Toiber
• 2017 - 2019: Master student
  • Human Physiology Lab, MIPT, Dolgoprudny, Russia
  • Thesis: Electrical activity modeling in the myocardium using human ventricular tissue experimental measurements of the action potentials
  • Supervisor: R.A. Syunyaev, PhD
• 2016 - 2017: Bachelor student
  • Human Physiology Lab, MIPT, Dolgoprudny, Russia
  • Thesis: Genetic algorithms application for searching the optimal set of parameters for models of electrical activity of cardiomyocytes
  • Supervisor: R.A. Syunyaev, PhD

Skills

BIOINFORMATICS SKILLS

• Bulk transcriptomics: data processing (Salmon, STAR, Hisat2, Samtools, nf-core/rnaseq), differential expression analysis (DESeq2), over-representation and pathway analyses (clusterProfiler, SPIA).
• Single-cell transcriptomics: downstream analysis with Seurat package.
• Metabolomics/Lipidomics: raw data processing (XCMS), differential abundance analysis, partial least-squares discriminant analysis (PLS-DA)
• Hi-C: processing with Distiller, downstream analysis (cooler, cooltools), TAD calling (Armatus, lavaburst)
• Variant calling: VarScan2, GATK, mitoAnalyzer

DATA SCIENCE SKILLS

• ML: sklearn, xgboost
• Deep Learning: pytorch, tensorflow

PROGRAMMING SKILLS

• R, Python, C, C++, MATLAB/SIMULINK, MPI, OpenMP, CUDA, Git, TEX, LATEX

LABORATORY SKILLS

• DNA purification, agarose gel electrophoresis, PCR.

Publications

Publications

Conference presentations

1. 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. July 2022

2. 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. May 2022

3. 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) August 2021

4. Smirnov DN, Khrameeva EE. “Topologically Associating Domain optimal set prediction using Armatus software” – Oral presentation at ITASb, online conference, April 2020

5. Smirnov DN, Belyakova GA, Syunyaev RA, Gusev OA, Deviatiiarov RM, Efimov IR. “Personalized ionic models of cardiomyocytes on the basis of molecular data and genetic algorithms” - poster presentation at Biomembranes 2018, Dolgoprudny, Russia October 2019

6. D. Smirnov, M. Zhukova, R. Syunyaev. “Genetic algorithms application for searching the optimal set of parameters for electrical activity models of cardiomyocytes” - oral presentation at 49th Mathematics.Computing.Education International Conference, Dubna, Russia Feb 2018.

7. D. Smirnov, R. Syunyaev. “Genetic algorithms application for searching the optimal set of parameters for electrical activity models of cardiomyocytes” - oral presentation at 59th MIPT Scientific Conference, Dolgoprudny, Russia Nov 2016.

Courses

49th IFF Spring School Physics of Life” (Julich, Germany)

References

Prof. Ekaterina Khrameeva
Assistant Professor
Khrameeva Lab, Skoltech
Nobel 3, Moscow, Moscow Region, 121205, Russia
email: ekhrameeva@gmail.com

Prof. Deborah Toiber
Associate Professor
Toiber Lab, Ben-Gurion University of the Negev
653 Beer-Sheva, Israel
email: toiber@bgu.ac.il