Vitalii Kleshchevnikov
PhD fellow
I study how regulatory states and tissue context define cell identity, using large-scale genomics data & bayesian modelling.
I study how regulatory states and tissue context define cell identity, with the aim to more comprehensively understand the development of the human cerebral cortex, and to investigate the re-use of regulatory programmes and transcription factor logic across human tissues. To this end, we are using large-scale genomics data & bayesian modelling – the work in done in collaboration with multiple groups across the institute.
My timeline
PhD @ Wellcome Sanger Institute & University of Cambridge
Visiting Scientist @ Parts group, Wellcome Sanger Institute
Intern @ Petsalaki group, European Bioinformatics Institute
MSc @ Taras Shevchenko National University of Kyiv
Intern @ Colin Stewart lab, Institute of Medical Biology, A*STAR
BUSS Summer School @ University of Zurich & ETH Zurich
BSc @ Taras Shevchenko National University of Kyiv
My publications
Overview of the spatial mapping approach and the workflow which are enabled by cell2location. From left to right: Single-cell RNA-seq and spatial transcriptomics profiles are generated from the same tissue (1). Cell2location takes reference cell type signatures derived from scRNA-seq and spatial transcriptomics data as input (2, 3). The model then decomposes spatially resolved multi-cell RNA counts matrices into the reference signatures, thereby establishing a spatial mapping of cell types (4).
Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map. This work suggests that the identity of cortical astrocytes is a combination of 2 gene expression programmes: subtype and layer-specific.
Connect with me on Twitter
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This is a beautiful paper due to its mathematical formulation of cellular reprogramming paradox: how can an unstable dynamical state be an attractor when only 4 genes are overexposed? The introduction is worth reading on its own, never mind the proposed elegant solution! https://twitter.com/PhysRevResearch/status/1514064079178117124
Dynamical systems theory of cellular reprogramming, Yuuki Matsushita, Tetsuhiro S. Hatakeyama, and Kunihiko Kaneko #biophysics #statisticalphysics https://go.aps.org/37IgIAu
Meanwhile, the single cell field
