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Artem Kasianov

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I am a bioinformatician with a strong interest in Molecular evolution, Human population genetics, and history. I earned my PhD in Molecular Biology in 2012 from V.A. Engelhardt's Institute of Molecular Biology in Moscow, Russia. Additionally, I hold a Master's degree in Applied Mathematics and Informatics. Thus, my first experience with biological sciences was connected with developing pipelines, software, and algorithms for processing NGS data. I have also been involved in numerous de novo genome and transcriptome assembly projects. My favorites of them are the Shepherd's Purse (C.bursa-pastoris), buckwheat (F.esculentum) genome assembly project, medicinal leech (H. medicinalis) transcriptome and genome assembly project, transcriptome assembly of land snail (H.lucorum) and grey whale (E. robustus).

From 2012 to 2022, I worked in several Russian Academy of Sciences institutes. However, especially important for me was participation in the work of the Laboratory of Evolutionary Genomics, Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University. During that period of my career, I had a lot of experience in genome assembly topic and clearly understood that obtaining a perfect genome sequence is not a final point in biological studies. Main consumers of new non-model species de novo assembled sequences were colleagues involved in evolutionary studies. Consequently, I quickly became involved in such analyses and developed a keen interest in molecular evolution, which, along with my passion for historical sciences, eventually formed the basis of my current scientific interests.

Since 2024, I have been a member of the HumanEVOL group, where I have become involved in research projects focusing on the population history of human populations living in the Okavango River Basin. Additionally, I am greatly interested in immunogenetics and in developing bioinformatics algorithms and approaches for addressing population genetics questions.

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My Publications

Penin, A.A., Kasianov, A.S., Klepikova, A.V. et al. Origin and diversity of Capsella bursa-pastoris from the genomic point of view. BMC Biol 22, 52 (2024).

doi: 10.1186/s12915-024-01832-1

Kasianova, A.M., Penin, A.A., Schelkunov, M.I., Kasianov, A.S., Logacheva, M.D., Klepikova, A.V. Trans2express – de novo transcriptome assembly pipeline optimized for gene expression analysis. bioRxiv 2024.01.11.575187 (2024).

doi: 10.1101/2024.01.11.575187

Krinitsina, A.A., Omelchenko, D.O., Kasianov, A.S., Karaseva, V.S., Selezneva, Y.M., Chesnokova, O.V., Shirobokov, V.A., Polevova, S.V., Severova, E.E. Aerobiological Monitoring and Metabarcoding of Grass Pollen. Plants 12, 2351 (2023).

doi: 10.3390/plants12122351

Subkhankulova, T., Camargo Sosa, K., Uroshlev, L.A., Nikaido, M., Shriever, N., Kasianov, A.S., Yang, X., Rodrigues, F.S.L.M., Carney, T.J., Bavister, G., Schwetlick, H., Dawes, J.H.P., Rocco, A., Makeev, V.J. and Kelsh, R.N. Zebrafish pigment cells develop directly from persistent highly multipotent progenitors. Nature communications 14, 1258 (2023).

doi: 10.1038/s41467-023-36876-4

Kasianov, A.S., Klepikova, A.V., Mayorov, A.V., Buzanov, G.S., Logacheva, M.D. and Penin, A.A. Interspecific comparison of gene expression profiles using machine learning. PLoS Computational Biology 19(1), e1010743 (2023).

doi: 10.1371/journal.pcbi.1010743

Omelchenko, D.O., Krinitsina, A.A., Kasianov, A.S., Speranskaya, A.S., Chesnokova, O.V., Polevova, S.V. and Severova, E.E. Assessment of ITS1, ITS2, 5′-ETS, and trnL-F DNA Barcodes for Metabarcoding of Poaceae Pollen. Diversity 14, 191 (2022).

doi: 10.3390/d14030191

Klepikova, A.V., Shnayder, E.D., Kasianov, A.S., Remizowa, M.V., Sokoloff D.D. and Penin, A.A. lepidium-like, a Naturally Occurring Mutant of Capsella bursa-pastoris, and Its Implications on the Evolution of Petal Loss in Cruciferae. Front. Plant Sci., Sec. Plant Development and EvoDevo Volume 12 (2021).

doi: 10.3389/fpls.2021.714711

Klepikova, A.V., Kasianov, A.S., Ezhova, M.A., Penin, A.A. and Logacheva, M.D. Transcriptome atlas of Phalaenopsis equestris. PeerJ 9:e12600 (2021).

doi: 10.7717/peerj.12600

Lavrov, K.V., Novikov, A.D., Kasianov, A.S., Toshchakov, S.V., Korzhenkov, A.A. and Yanenko, A.S. Draft Genome Sequence of Rhodococcus qingshengii (Formerly erythropolis) TA37, a First-Generation Biocatalyst for Synthesis of Functionalized Acrylamides. Microbiology Resource Announcements 10, 50 (2021).

doi: 10.1128/MRA.01057-21

Novikov, A.D., Lavrov, K.V., Kasianov, A.S., Topchiy, M.A., Gerasimova, T.V. and Yanenko, A.S. Complete Genome Sequence of Rhodococcus sp. Strain M8, a Platform Strain for Acrylic Monomer Production. Microbiology Resource Announcements 10, 10 (2021).

doi: 10.1128/mra.01314-20

Novikov, A.D., Lavrov, K.V., Kasianov, A.S., Korzhenkov, A.A., Gubanova, T.A. and Yanenko, A.S. Draft Genome Sequence of Rhodococcus erythropolis HX7, a Psychrotolerant Soil-Derived Oil Degrader.” Microbiology Resource Announcements 10, 3 (2021).

doi: 10.1128/mra.01353-20

Slezina, M.P., Istomina, E.A., Korostyleva, T.V., Kovtun, A.S., Kasianov, A.S., Konopkin, A.A., Shcherbakova, L.A. and Odintsova, T.I. Molecular Insights into the Role of Cysteine-Rich Peptides in Induced Resistance to Fusarium oxysporum Infection in Tomato Based on Transcriptome Profiling. Int. J. Mol. Sci. 22(11), 5741 (2021).

doi: 10.3390/ijms22115741

Penin, A.A., Kasianov, A.S., Klepikova, A.V., Kirov, I.V., Gerasimov, E.S., Fesenko, A.N. and Logacheva, M.D. High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum. Front Plant Sci. 12, 612382 (2021).

doi: 10.3389/fpls.2021.612382

Babenko, V.V., Podgorny, O.V., Manuvera, V.A., Kasianov, A.S., Manolov, A.I., Grafskaia, E.N., Shirokov, D.A., Kurdyumov, A.S., Vinogradov, D.V., Nikitina, A.S., Kovalchuk, S.I., Anikanov, N.A., Butenko, I.O., Pobeguts, O.V., Matyushkina, D.S., Rakitina, D.V., Kostryukova, E.S., Zgoda, V.G., Baskova, I.P., Trukhan, V.M., Gelfand, M.S., Govorun, V.M., Schiöth, H.B. and Lazarev, V.N. Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches. BMC Genomics 21, 331 (2020).

doi: 10.1186/s12864-020-6748-0

Veselovsky, V.A., Dyachkova, M.S., Menyaylo, E.A., Polyaeva, P.S., Olekhnovich, E.I., Shitikov, E.A., Bespiatykh, D.A., Semashko, T.A., Kasianov, A.S., Ilina, E.N., Danilenko, V.N. and Klimina, K.M. Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors. Frontiers in Immunology 11, 595877 (2020).

doi: 10.3389/fimmu.2020.595877

Valyaeva, A.A., Zharikova, A.A., Kasianov, A.S., Vassetzky, Y.S. and Sheval, E.V. Expression of SARS-CoV-2 entry factors in lung epithelial stem cells and its potential implications for COVID-19. Scientific Reports 10, 17772 (2020).

doi: 10.1038/s41598-020-74598-5

Morozova, I., Kasianov, A., Bruskin, S., Neukamm, J., Molak, M., Batieva, E., Pudło, A., Rühli, F.J. and Schuenemann, V.J. New ancient Eastern European Yersinia pestis genomes illuminate the dispersal of plague in Europe. Phil. Trans. R. Soc. B375, 20190569 (2020).

doi: 10.1098/rstb.2019.0569

Bezmenova, A.V., Zvyagina, E.A., Fedotova, A.V., Kasianov, A.S., Neretina, T.V., Penin, A.A., Bazykin, G.A. and Kondrashov, A.S. Rapid accumulation of mutations in growing mycelia of a hypervariable fungus Schizophyllum commune. Molecular Biology and Evolution 37, 8 (2020).

doi: 10.1093/molbev/msaa083

Klepikova, A.V. and Kasianov, A.S. An Update to the TraVA Database: Time Series of Capsella bursa-pastoris Shoot Apical Meristems during Transition to Flowering.” Data 5(3), 58 (2020).

doi: 10.3390/data5030058

Klimina, K.M., Voroshilova, V.N., Poluektova, E.U., Veselovsky, V.A., Yunes, R.A., Kovtun, A.S., Kudryavtseva, A.V., Kasianov, A.S. and Danilenko, V.N. Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota. Toxins 12(6), 388 (2020).

doi: 10.3390/toxins12060388

Logacheva, M.D., Schelkunov, M.I., Fesenko, A.N., Kasianov, A.S. and Penin, A.A. Mitochondrial Genome of Fagopyrum esculentum and the Genetic Diversity of Extranuclear Genomes in Buckwheat. Plants 9(5), 618 (2020).

doi: 10.3390/plants9050618

Omelchenko, D.O., Makarenko, M.S., Kasianov, A.S., Schelkunov, M.I., Logacheva, M.D. and Penin, A.A. Assembly and Analysis of the Complete Mitochondrial Genome of Capsella bursa-pastoris. Plants 9(4), 469 (2020).

doi: 10.3390/plants9040469

Orekhov, A.N., Sukhorukov, V.N., Nikiforov, N.G., Kubekina, M.V., Sobenin, I.A., Foxx, K.K., Pintus, S., Stegmaier, P., Stelmashenko, D., Kel, A., Poznyak, A.V., Wu, W.K., Kasianov, A.S., Makeev, V.Y., Manabe, I. and Oishi, Y. Signaling Pathways Potentially Responsible for Foam Cell Formation: Cholesterol Accumulation or Inflammatory Response—What is First? International Journal of Molecular Sciences 21(8), 2716 (2020).

doi: 10.3390/ijms21082716

Liang, R., Arif, T., Kalmykova, S., Kasianov, A., Lin, M., Menon, V., Qiu, J., Bernitz, J.M., Moore, K., Lin, F., Benson, D.L., Tzavaras, N., Mahajan, M., Papatsenko, D. and Ghaffari, S. Restraining Lysosomal Activity Preserves Hematopoietic Stem Cell Quiescence and Potency.” Cell Stem Cell 26 (3), 299-301 (2020).

doi: 10.1016/j.stem.2020.01.013

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