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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We're recruiting a PhD student
Interested in developmental & stem cell biology?
Want to live in London?
Like to be part of @TheCrick fantastic graduate student programme?
Applications are open. Deadline Nov 11
https://www.crick.ac.uk/careers-study/students/phd-students/phd-student-recruitment/phd-student-positions/what-controls-the-speed-of-embryonic-development
Final version of the Baysor publication is now online! In the new version we added 3D segmentation, analysis of cell compartments and a MERFISH gut dataset, thanks for to Jeff Moffit, Rosalind Xu, and Paolo Cadinu! And the methods are fully rewritten.
https://www.nature.com/articles/s41587-021-01044-w
Spatial transcriptomics is key to learn how tissues function and cancer develops.
Here we present PoSTcode to get better data from In Situ Sequencing experiments:
* up to 50% higher yield
* less confusion of molecules
* fewer artefacts
https://www.biorxiv.org/content/10.1101/2021.10.12.464086v1
