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aleksandragalitsina

Aleksandra Galitsyna

PhD student

Aleksandra is working at the intersection of chromatin biology and data analysis. Her current research is focused on single-cell DNA interactome analysis and application of advanced machine learning algorithms to unraveling the problem of genomic structure formation in various species.

Aleksandra graduated from Moscow State University, Faculty of Bioengineering and Bioinformatics in 2017, and since then continues to deepen her knowledge and understanding of chromatin structure formation under the supervision of Professor Mikhail Gelfand.

Research advisor: Professor Mikhail Gelfand

Program entry year: 2017

Research project: Chromatin folding in individual cells

Research interestschromatin topology, computational biology, NGS, single-cell Hi-C, data analysis

Publications: 

  • Order and stochasticity in the folding of individual Drosophila genomes.
    S. Ulianov*, V. Zakharova*, A. Galitsyna*, P. Kos*, K. Polovnikov, I. Flyamer, E. Mikhaleva, E. Khrameeva, D. Germini, M. Logacheva, et al. Nature Communications 12, 1–17, DOI: 10.1038/s41467-020-20292-z 
  • A machine learning framework for the prediction of chromatin folding in Drosophila using epigenetic features.
    M. Rozenwald, A. Galitsyna, G.Sapunov, E. Khrameeva, M. Gelfand.
    PeerJ Computer Science 6,e307 (2020), DOI: 10.7717/peerj-cs.307
  • HiChew: a Tool for TAD Clustering in Embryogenesis
    N. Bykov, O. Sigalova, M. Gelfand and A. Galitsyna
    Bioinformatics Research and Applications (Springer International Publishing, Cham), ISBRA 2020. Lecture Notes in Computer Science, vol 12304. Springer, Cham., DOI: 10.1007/978-3-030-57821-3_37
  • Studying RNA – DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics.
    A. Gavrilov, A. Zharikova, A. Galitsyna, A. Luzhin, N. Rubanova, A. Golov,  N. Petrova, M. Logacheva, O. Kantidze, S. Ulianov, M. Magnitov, A. Mironov and S. Razin.
    Nucleic Acids Research, 2020, 48, 6699–6714, DOI: 10.1093/nar/gkaa457
  • Cumulative contact frequency of a chromatin region is an intrinsic property linked to its function.
    M. Samborskaia*, A. Galitsyna*, I. Pletenev, A. Trofimova, A. Mironov, M. Gelfand and E. Khrameeva.
    PeerJ 2020, 8, e9566, DOI: 10.7717/peerj.9566.
  • Nuclear lamina integrity is required for proper spatial organization of chromatin in Drosophila.
    S. Ulyanov, S. Doronin, E. Khrameeva, P. Kos, A. Luzhin, S. Starikov, A. Galitsyna, V. Nenasheva, A. Ilyin, I. Flyamer, E. Mikhaleva, M. Logacheva, M. Gelfand, A. Chertovich, A. Gavrilov, S. Razin, Y. Shevelyov.
    Nature Communications, 2019, 10(1), DOI: 10.1038/s41467-019-09185-y
  • Evolution of the genome 3D organization: comparison of fused and segregated globin clusters.
    Kovina A.P., Petrova N.V., Gushchanskaya E.S., Dolgushin K.V., Gerasimov E.S., Galitsyna A.A., Penin A.A., Flyamer I.M., Ioudinkova E.S., Gavrilov A.A., Vassetzky Y.S., Ulianov, S.V., Iarovaia O.V., Razin S.V.
    Molecular Biology and Evolution, 2017, 34(6):1492–1504, DOI: 10.1093/molbev/msx100
  • “Mirror reads” in Hi-C data.
    Galitsyna A.A., Khrameeva E.E., Razin S.V., Gelfand M.S., Gavrilov A.A.
    Genomic and Computational Biology, 2017, 3(1):e36, DOI: 10.18547/gcb.2017.vol3.iss1.e36
  • Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes of large-scale chromatin spatial structure.
    Ulianov S.V.*, Galitsyna A.A.*, Golov A., Flyamer I.M., Khrameeva E.E., Imakaev M.V., Abdennur N.A., Gelfand M.S., Gavrilov A.A., Razin S.V. Epigenetics & Chromatin, 2017, 10(1):35, DOI: 10.1186/s13072-017-0142-4

* – co-first authors with equal contributions

Conference presentations:

  • Oral presentation “Large-scale analysis of RNA-DNA interactions” 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM’2018), Madrid, Spain, 2-6 December 2018
    Galitsyna A.A. et al.
  • Poster presentation “Chromatin properties of individual cells of Drosophila melanogaster” MIT-Skoltech Conference “Collaborative Solutions for Next Generation Education, Science
    and Technology”, Moscow, Russia, 3-6 December
    Galitsyna A.A. et al.
  • Poster presentation “Comparison of TAD callers for Hi-C data” at the European Student Council Symposium 2018, Athens, Greece, 7-8 September 2018
    Mylarshchikov D.E., Galitsyna A.A.
  • Poster presentation“Single-cell Hi-C data analysis of Drosophila melanogaster” at the 17th European Conference on Computational Biology 2018, Athens, Greece, 8-12 September 2018
    Galitsyna A.A., Zakharova V.V., Khrameeva E.E., Razin S.V., Gelfand M.S., Ulyanov S.V.
  • Poster presentation“RNA-DNA interactome of human cells Poster presentation” at Nuclear Landscapes 2018, Warsaw, Poland, 14-16 September 2018
    Galitsyna A.A., Zharikova A.A., Logacheva M.D., Razin S.V., Mironov A.A., Gavrilov A.A.
  • Oral presentation «Single-cell Hi-C in Drosophila», co-reporter of oral presentation «Whole-genome RNA-DNA interactions analysis», co-reporter of poster presentation «TAD callers comparison» at ITAS 2018, Kazan, Russia, 25-30 September.

Grants: 

  • 2018: Systems biology Fellowship Program at Skoltech Center of Life Sciences
  • 2019: Russian Foundation for Basic Research (RFBR) grant for PhD students for “Chromatin interactions in individual cells: development of bioinformatics tools and data analysis”

Awards:

  • Prizewinner at Biohack-2018, Saint Petersburg hackathon in computational biology (team competition)
  • Best poster presentation at Nuclear Landscapes 2018 conference, Warsaw, Poland
  • Best oral presentation at ITaS’2018 conference, Innopolis, Kazan, Russia
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