Vitalii Kleshchevnikov
PhD Student
I am investigating how gene expression states of cells are linked to cell contact neighbourhoods in tissues. Cataloging and comparing the patterns of cell-cell contacts, their transcriptional dependencies and consequences is essential for understanding the molecular rules that govern both the structure of tissues and the context-dependent cell functions.
I use single-cell transcriptomics of isolated cells, highly-multiplexed large-scale in-situ quantification of gene expression and systems biology tools to characterise transcriptional states of neighbouring cells. To interpret scRNA-seq & spatial gene expression and ask quantitative questions I develop probabilistic models of the underlying generative process.
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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Got a really nice time-lapse video of my DNA gel today as the bands moved through the agarose 😊
New paper from the lab: we used massively parallel reporter assays (MPRA) to test enhancer activity of H3K27Ac peaks, ATAC-seq peaks, and tiled short seqs across melanoma cultures, and compared their activity with deep learning predictions. Great work by @David_Mauduit et al. ! https://twitter.com/david_mauduit/status/1420311249955459077
Our work on enhancer activity in melanoma subtypes is now available on @biorxivpreprint!
https://bit.ly/3iXNM9A
Thank you to everyone from @steinaerts lab who contributed.
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In the latest issue! An atlas of protein-protein interactions across mouse tissues http://dlvr.it/S4S3DZ