A5090973325- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- Immune cells in cancer
- Advanced Fluorescence Microscopy Techniques
- Legume Nitrogen Fixing Symbiosis
- Neuroinflammation and Neurodegeneration Mechanisms
- CRISPR and Genetic Engineering
- Cell Image Analysis Techniques
- RNA Research and Splicing
- Biochemical and Structural Characterization
- Erythrocyte Function and Pathophysiology
- Microbial Metabolites in Food Biotechnology
- Cancer therapeutics and mechanisms
- Toxin Mechanisms and Immunotoxins
- Advancements in Transdermal Drug Delivery
- Lipid metabolism and biosynthesis
- Neonatal Respiratory Health Research
- Metabolomics and Mass Spectrometry Studies
- Antimicrobial Peptides and Activities
- Bacterial Genetics and Biotechnology
- Synthesis and Biological Activity
- Advanced Proteomics Techniques and Applications
- Cancer-related molecular mechanisms research
- Retinal Development and Disorders
- Pluripotent Stem Cells Research
École Polytechnique Fédérale de Lausanne
2020-2024
Lomonosov Moscow State University
2016-2019
Human cells produce thousands of lipids that change during cell differentiation and can vary across individual the same type. However, we are only starting to characterize function these cell-to-cell differences in lipid composition. Here, measured lipidomes transcriptomes human dermal fibroblasts by coupling high-resolution mass spectrometry imaging with single-cell transcriptomics. We found variations specific metabolic pathways contribute establishment states involved organization skin...
In order to accelerate drug discovery, a simple, reliable, and cost-effective system for high-throughput identification of potential antibiotic mechanism action is required. To facilitate such screening new antibiotics, we created double-reporter not only antimicrobial activity detection but also simultaneous sorting antimicrobials into those that cause ribosome stalling induce the SOS response due DNA damage. this reporter system, red fluorescent protein gene rfp was placed under control...
Abstract Ribosome-synthesized post-translationally modified peptides (RiPPs) represent a rapidly expanding class of natural products with various biological activities. Linear azol(in)e-containing (LAPs) comprise subclass RiPPs that display outstanding diversity mechanisms action while sharing common structural features. Here, we report the discovery new LAP biosynthetic gene cluster in genome Rhizobium Pop5, which encodes precursor peptide and modification machinery phazolicin (PHZ) – an...
Across a range of biological processes, cells undergo coordinated changes in gene expression, resulting transcriptome dynamics that unfold within low-dimensional manifold. Single-cell RNA-sequencing (scRNA-seq) only measures temporal snapshots expression. However, information on the underlying can be extracted using RNA velocity, which models unspliced and spliced abundances to estimate rate change Available velocity algorithms fragile rely heuristics lack statistical control. Moreover,...
The mammalian brain develops through a complex interplay of spatial cues generated by diffusible morphogens, cell-cell interactions, and intrinsic genetic programs that result in the generation likely more than thousand distinct cell types. Therefore, complete understanding development requires systematic mapping states covering entire relevant spatiotemporal range. Here we report comprehensive single-cell transcriptome atlas mouse spanning from gastrulation to birth. We identified almost...
Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-RPE) are a promising cell source to treat age-related macular degeneration (AMD). Despite several ongoing clinical studies, detailed mapping of transient cellular states during in vitro differentiation has not been performed. Here, we conduct single-cell transcriptomic profiling an hESC-RPE protocol that developed for use. Differentiation progressed through culture diversification recapitulating early development,...
Identifying spot-like structures in large and noisy microscopy images is a crucial step to produce high quality results various life-science applications. Imaging-based spatial transcriptomics (iST) methods, particular, critically depend on the precise detection of millions transcripts with low signal-to-noise ratio. Despite advances computer vision that have revolutionized many biological imaging tasks, currently adopted spot techniques are mostly still based classical signal processing...
Abstract Across biological systems, cells undergo coordinated changes in gene expression, resulting transcriptome dynamics that unfold within a low-dimensional manifold. While can be extracted using RNA velocity, these algorithms fragile and rely on heuristics lacking statistical control. Moreover, the estimated vector field is not dynamically consistent with traversed expression To address challenges, we introduce Bayesian model of velocity couples manifold estimation reformulated, unified...
ABSTRACT The embryonic neural tube is the origin of entire adult nervous system, and disturbances in its development cause life-threatening birth defects. However, study mammalian limited by lack physiologically realistic three-dimensional (3D) vitro models. Here, we report a self-organizing 3D organoid model derived from single mouse stem cells that exhibits an vivo-like tissue architecture, cell type composition anterior-posterior (AP) patterning. Moreover, maturation organoids showed...
Human cells produce thousands of lipids that impact a wide range biological processes in ways we are only starting to characterize. The cellular composition changes during differentiation events and also varies across individual the same type. Yet, precise differences lipid directly affect cell phenotypes remain unknown. Here have measured lipidomes transcriptomes human dermal fibroblasts by coupling high-resolution mass spectrometry imaging single-cell transcriptomics. We found cell-to-cell...
Embryo development entails the formation of anatomical structures with distinct biochemical compositions. Compared wealth knowledge on gene regulation, our understanding metabolic programs operating during embryogenesis is limited. Mass spectrometry imaging (MSI) has potential to map distribution metabolites across embryo development. Here, we established an analytical framework for joint analysis large MSI datasets that allows construction multi-dimensional metabolomic atlases. Employing...
ABSTRACT Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a rapidly expanding largely untapped class of natural products with various biological activities. Linear azol(in)e-containing (LAPs) comprise subclass RiPPs that display an outstanding diversity mechanisms action while sharing common structural features. Here, we report the discovery new LAP biosynthetic gene cluster in genome Rhizobium sp. Pop5, which encodes precursor peptide modification machinery...
suggest that the sequence of protein uL4 loop determines whether PHS compound can bind to ribosome and provides basis for species-specific activity ribosome-targeting antibiotics.Conclusions: its predicted homologs from genomes other bacterial species expand known diversity LAPs, which potentially be used as biocontrol agents needs agriculture.