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Andrey Tomarovsky

Bioinformatician
Institute of Molecular and Cell Biology SB RAS
andrey.tomarovsky@gmail.com


About Me

Software enthusiast in bioinformatics based in Novosibirsk, Russia

👨🏻‍🎓 Education

Sep 2021 - Jul 2025 PhD in Genetics
Novosibirsk State University, Novosibirsk, Russia
PhD thesis: “Consequences of interspecific hybridization and phylogenetic relationships in the genus Martes (Family Mustelidae)”
Sep 2019 - Jul 2021 MS in Bioinformatics
Saint-Petersburg State University, St. Petersburg, Russia
MS thesis: “Assembly and annotation of the sable (Martes zibellina) and pine marten (Martes martes) genomes”
Sep 2015 - Jul 2019 BS in Biotechnologies
Belgorod State National Research University, Belgorod, Russia

🏆 Work experience

May 2023 - Present Junior Researcher | Bioinformatician
Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
Laboratory of Diversity and Evolution of Genomes · Full-time
Comparative genomics of Mustelidae family species
Apr 2021 - Nov 2023 Junior System Administrator
Moscow State University, Moscow, Russia
Faculty of Bioengineering and Bioinformatics · Part-time
Administration of “Makarich” computational cluster
Feb 2022 - May 2023 Junior Researcher | Bioinformatician
Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
Laboratory of Animal Cytogenetics, Department of Diversity and Evolution of Genomes · Part-time
Comparative genomics of Mustelidae family species
Mar 2021 - Dec 2022 Research Programmer | Bioinformatician
ITMO University, St. Petersburg, Russia
Research Center for Genomic Diversity, International Laboratory “Computer Technologies” · Contract
Genomics of Martes species (fam. Mustelidae)
Feb 2021 - Present Visiting Lecturer & Technical Specialist
Blastim’s Online Courses · Part-time
Visiting lecturer:
- Introduction to Linux for Bioinformatics
- Snakemake for Bioinformatics
Technical & software support, cluster administration:
- Python for Data Analysis in Science
- Analyzing NGS Data
- Analyzing RNA-seq Data
- Statistics, R and Data Analysis

🛠 Skills

Languages Russian – native, English – full professional proficiency
OS Linux, Windows
Shell Bash; Shell tools: vim, grep, awk, sed, etc.
Programming Python, R
Python libraries Biopython, Matplotlib, Numpy, Pandas, Ete3
R libraries ggplot2, dplyr, readxl
Workflow managers Snakemake
Workload managers Slurm, PBS
Container platforms Apptainer/Singularity, Docker
Package managers Conda/Mamba, pip, CRAN
Version control systems git
HPC ResOps experience with computations on HPC clusters
Others SQL, Circos, Tcl

🧐 Areas of expertise

Genome assembly De novo chromosome-level genome assembly of mammalian species using both short- and long-read sequencing technologies
Genome annotation Structural and functional genome annotation; De novo assembly and annotation of repetitive elements and transposable elements
Comparative genomics Comparative analysis of chromosomal rearrangements
Population genomics Assessment of genome-wide genetic diversity; Identification of runs of homozygosity and inbreeding estimation; Population structure analysis and ancestry inference; Reconstruction of population history
Phylogenomics Phylogenetic and phylogenomic analysis; Species tree inference and assessment of incomplete lineage sorting
Conservation biology Assessment of genomic consequences of population decline and isolation

📌 On The Side

Supervision of Master Students

Software Development

📝 Grants

2022 – 2023 Russian Scientific Foundation, grant № 22-24-01076: “Comparative genomics: analysis of evolutionary changes in syntenic chromosome blocks (Canidae and Cetartiodactyla) based on Hi-C maps”
2022 – 2023 Russian Scientific Foundation, grant № 19-14-00034-P: “Autosomes, sexual and additive chromosomes of vertebrates. Organization and Evolution”
2020 – 2022 Russian Foundation for Basic Research, grant № 20-04-00808 A: “Genomes and genetic diversity of mustelids (fam. Mustelidae) of Russia and South-Eastern Asia”

📝 Publications

  1. New genetic data on the Pleistocene Ovodov horses of Siberia
    Kusliy, M.A., Malikov, D.G., Klementiev, A.M., Samarina, S.A., Modina, S.A., Tishakova, K.V., Lemskaya, N.A., Serdyukova, N.A., Budenchuk, E.V., Yakovlev, A.V., Cheklyuev, P.A., Yurlova, A.A., Tomarovsky, A.A., Totikov, A.A., Nushtaev, Y.Y., Popova, K.O., Pavlov, I.S., Pavlova, N.I., Protopopov, A.V., Graphodatsky, A.S., Vorobieva, N.V., Molodtseva, A.S.
    Quaternary Science Reviews, 2026; Vol. 372. P. 109696
    DOI Q1, IF=3.3

  2. Novel Chromosome-Length Genome Assemblies of Three Distinct Subspecies of Pine Marten, Sable, and Yellow-Throated Marten (Genus Martes, Family Mustelidae)
    Tomarovsky, A.A., Khan, R., Dudchenko, O., Beklemisheva, V.R., Perelman, P.L., Totikov, A.A., Serdyukova, N.A., Bulyonkova, T.M., Pobedintseva, M., Abramov, A.V., Weisz, D., Yakupova, A., Zhuk, A., Graphodatsky, A.S., Powell, R., Aiden, E., Koepfli, K.-P., Kliver, S
    Journal of Heredity, 2025; esaf101
    DOI Q1, IF=2.5

  3. Genomics of sable (Martes zibellina) × pine marten (Martes martes) hybridization
    Tomarovsky, A.A., Totikov, A.A., Bulyonkova, T.M., Perelman, P.L., Abramov, A.V., Serdyukova, N.A., Yakupova, A.R., Prokopov, D., Beklemisheva, V.R., Sinding, M.-H., Davletshina, G., Pobedintseva, M., Krasheninnikova, K., Foerster, D., Mukhacheva, A.S., Mironova, A., Sidorov, M., Nie, W., Wang, J., Romanenko, S.A., Proskurykova, A., Ferguson-Smith, M., Yang, F., Cherkasov, N., Balanovska, E., Gilbert, T.P., Okhlopkov, I.M., Zhuk, A., Graphodatsky, A.S., Powell, R., Koepfli, K.-P., Kliver, S
    Genome Biology and Evolution, 2026
    DOI Q1, IF=3.3

  4. Chromosome length genome assembly of the stone marten (Martes foina, Mustelidae): a new view on one of the cornerstones in carnivore cytogenetics
    Tomarovsky, A.A., Khan, R., Dudchenko, O., Totikov, A.A., Serdyukova, N.A., Weisz, D., Vorobieva, N.V., Bulyonkova, T., Abramov, A.V., Nie, W., Wang, J., Romanenko, S.A., Proskuryakova, A.A., Cherkasov, N., Ferguson-Smith, M.A., Yang, F., Balanovskaya, E., Gilbert, M.T.P., Graphodatsky, A.S., Aiden, E.L., Powell, R., Koepfli, K.-P., Perelman, P.L., Kliver, S.
    Journal of Heredity, 2025; esaf001
    DOI Q1, IF=2.5

  5. Comparative genomics and phylogenomics of the Mustelinae lineage (Mustelidae, Carnivora)
    Totikov, A.A., Tomarovsky, A.A., Perelman, P.L., Bulyonkova, T.M., Serdyukova, N.A., Yakupova, A.R., Mohr, D., Foerster, D.W., Grau Jipoulou, J.H., Beklemisheva, V.R., Sidorov, M., Miranda, I., Farelo, L., Abramov A.V., Krasheninnikova, K., Mukhacheva, A.S., Panov, V.V., Balanovska, E., Cherkasov, N., Zub, K., Scott, A.F., Melo-Ferreira, J., Okhlopkov, I.M., Zhuk, A., Koepfli, K.-P., Graphodatsky, A.S., Kliver, S.
    Genome Biology and Evolution, 2026
    DOI Q1, IF=3.3

  6. Review of heterozygosity visualization approaches in the context of conservation research
    Tomarovsky, A.A., Totikov, A.A., Yakupova, A.R., Graphodatsky, A.S., Kliver, S.
    Ecological Genetics, 2023. Vol. 21. N. 4. P. 383-400 (ru)
    DOI Q4, IF=0.2

  7. Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes)
    Kliver, S., Houck, M.L., Perelman, P.L., Totikov, A.A., Tomarovsky, A.A., Dudchenko, O., Omer, A.D., Colaric, Z., Weisz, D., Aiden, E.L., Chan, S., Hastie, A., Komissarov, A., Ryder, O.A., Graphodatsky, A.S., Johnson, W.E., Maldonado, J.E., Pukazhenthi, B.S., Marinari, P.E., Wildt, D.E., Koepfli, K.-P.
    Journal of Heredity, 2023; esad035
    DOI Q1, IF=2.5

  8. Review of population history reconstruction methods in conservation biology
    Totikov, A.A., Tomarovsky, A.A., Yakupova, A.R., Graphodatsky, A.S., Kliver, S.
    Ecological Genetics, 2023. Vol. 21. N. 1. P. 85-102 (ru)
    DOI Q4, IF=0.2

  9. Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal
    Yakupova, A., Tomarovsky, A.A., Totikov, A.A., Beklemisheva, V., Logacheva, M., Perelman, P.L., Komissarov, A., Dobrynin, P., Krasheninnikova, K., Tamazian, G., Serdyukova, N.A., Rayko, M., Bulyonkova, T., Cherkasov, N., Pylev, V., Peterfeld, V., Penin, A., Balanovska, E., Lapidus, A., DNA Zoo Consortium, O'Brien, S.J., Graphodatsky, A., Koepfli, K.-P., Kliver, S.
    Genes, 2023. 14(3), 619
    DOI Q2, IF=2.8

  10. Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae
    Derežanin, L., Blažytė, A., Dobrynin, P., Duchêne, D.A., Grau, J.H., Jeon, S., Kliver, S., Koepfli, K.-P., Meneghini, D., Preick, M., Tomarovsky, A.A., Totikov, A.A., Fickel, J., Förster, D.W.
    Molecular Ecology, 2022, 31, 2898-2919
    DOI Q1, IF=3.9

  11. Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology
    Totikov, A.A., Tomarovsky, A.A., Prokopov, D., Yakupova, A., Bulyonkova, T., Derezanin, L., Rasskazov, D., Wolfsberger, W.W., Koepfli, K.-P., Oleksyk, T.K., Kliver, S.
    Genes, 2021, 12(9), 1336
    DOI Q2, IF=2.8

📝 Conferences

  1. Chromosome-level genome assembly of the Least Weasel (Mustela nivalis)
    Totikov, A., Tomarovsky, A., Perelman, P., Bulyonkova, T., Panov, V., DNA Zoo Consortium, Graphodatsky, A., Kliver, S.
    14th International Multiconference Bioinformatics of Genome Regulation and Structure / Systems Biology, August 5–10, 2024, Novosibirsk, Russia
    DOI

  2. Whole-genome data confirm the presence of crossover in hybrids of sable (M. zibellina) and pine marten (M. martes)
    Tomarovsky, A., Totikov, A., Perelman, P., Beklemisheva, V., Serdyukova, N., Bulyonkova, T., Sidorov, M., Mamaev, N., Okhlopkov, I., Mukhacheva, A., Koniaeva, K., Abramov, A., Graphodatsky, A., Kliver, S.
    14th International Multiconference Bioinformatics of Genome Regulation and Structure / Systems Biology, August 5–10, 2024, Novosibirsk, Russia
    DOI

  3. Assessment of heterozygosity levels of the Mustela species
    Totikov, A., Tomarovsky, A., Perelman, P., Beklemisheva, V., Serdyokova, N., Bulyonkova, T., Panov, V., Mukhacheva, A., Abramov, A., Graphodatsky, A., Kliver, S.
    International Conference “Chromosome-2023”, Novosibirsk, Russia
    DOI

  4. Assessment of heterozygosity levels of the sable (Martes zibellina), the pine marten (Martes martes), and their hybrids
    Tomarovsky, A., Totikov, A., Perelman, P., Beklemisheva, V., Serdyokova, N., Bulyonkova, T., Sidorov, M., Mamaev, N., Okhlopkov, I., Mukhacheva, A., Koniaeva, K., Abramov, A., Graphodatsky, A., Kliver, S.
    International Conference “Chromosome-2023”, Novosibirsk, Russia
    DOI

  5. Reconstruction of the demographic history for three populations of the least weasel (Mustela nivalis)
    Totikov, A., Tomarovsky, A., Perelman, P., Serdyokova, N., Beklemisheva, V., Bulyonkova, T., Zub, K., Panov, V., Mukhacheva, A., Abramov, A., Koepfli, K., Graphodatsky, A., Melo-Ferreira, J., Kliver, S.
    10th Moscow Conference on Computational Molecular Biology (MCCMB-2021), July 30 – August 2, 2021, Moscow, Russia
    ISBN

  6. Assembly and annotation of sable (Martes zibellina) and pine marten (Martes martes) genomes
    Tomarovsky, A., Totikov, A., Beklemisheva, V., Perelman, P., Serdyokova, N., Bulyonkova, T., Koniaeva, K., Abramov, A., Graphodatsky, A., Koepfli, K., Powell, R., Kliver, S.
    10th Moscow Conference on Computational Molecular Biology (MCCMB-2021)
    ISBN