A5045187327- CRISPR and Genetic Engineering
- Genetics, Bioinformatics, and Biomedical Research
- Epigenetics and DNA Methylation
- Single-cell and spatial transcriptomics
- Science, Research, and Medicine
- Zebrafish Biomedical Research Applications
- DNA Repair Mechanisms
- RNA Interference and Gene Delivery
- Cancer Genomics and Diagnostics
- Genetics, Aging, and Longevity in Model Organisms
- RNA and protein synthesis mechanisms
- Computational Drug Discovery Methods
- Congenital heart defects research
- Cosmology and Gravitation Theories
- Advanced biosensing and bioanalysis techniques
- Genomics and Chromatin Dynamics
- Gene Regulatory Network Analysis
- RNA Research and Splicing
- Cell Image Analysis Techniques
- Chromosomal and Genetic Variations
- Black Holes and Theoretical Physics
- melanin and skin pigmentation
- CAR-T cell therapy research
- Dyeing and Modifying Textile Fibers
- Diabetes and associated disorders
Charité - Universitätsmedizin Berlin
2023-2025
Max Delbrück Center
2017-2024
Royal Netherlands Academy of Arts and Sciences
2015-2017
University Medical Center Utrecht
2015-2017
International Centre for Genetic Engineering and Biotechnology
2017
Hubrecht Institute for Developmental Biology and Stem Cell Research
2016-2017
Cancer Genomics Centre
2015
Institut de Physique Théorique
2011
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2011
CEA Paris-Saclay
2011
The adult zebrafish heart has a high capacity for regeneration following injury. However, the composition of regenerative niche remained largely elusive. Here, we dissected diversity activated cell states in regenerating based on single-cell transcriptomics and spatiotemporal analysis. We observed emergence several transient with fibroblast characteristics injury, outlined proregenerative function collagen-12-expressing fibroblasts. To understand cascade events leading to regeneration,...
CRISPR/Cas9 (clustered regularly interspaced palindromic repeats/CRISPR-associated protein 9)-based DNA editing has rapidly evolved as an attractive tool to modify the genome. Although been extensively used manipulate germline in zygotes, its application postnatal gene remains incompletely characterized.
Abstract Early stages of embryogenesis depend on subcellular localization and transport maternal mRNA. However, systematic analysis these processes is hindered by a lack spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics labeling to perform the transcriptome during early zebrafish development. We measure spatial mRNA molecules within one-cell stage embryo, which allows us identify class mRNAs that are specifically localized at an...
ABSTRACT Regeneration-competent species possess the ability to reverse progression of severe diseases by restoring function damaged tissue. However, cellular dynamics underlying this capability remain unexplored. Here, we have used single-cell transcriptomics map de novo β-cell regeneration during induction and recovery from diabetes in zebrafish. We show that zebrafish has evolved two distinct types somatostatin-producing δ-cells, which term δ1- δ2-cells. Moreover, characterize a small...
DNA amplifications in cancer do not only harbor oncogenes. We sought to determine whether passenger coamplifications could create collateral therapeutic vulnerabilities. Through an analysis of >3,000 genomes followed by the interrogation CRISPR-Cas9 loss-of-function screens across >700 cell lines, we determined that are accompanied distinct dependency profiles. In a proof-of-principle study, demonstrate coamplification bona fide gene DEAD-Box Helicase 1 (DDX1) creates increased on mTOR...
Adult stem cells are important for tissue turnover and regeneration. However, in most adult systems it remains elusive how assume different functional states support spatially patterned architecture. Here, we dissected the diversity of neural zebrafish brain, an organ that is characterized by pronounced zonation high regenerative capacity. We combined single-cell transcriptomics brain regions with massively parallel lineage tracing vivo RNA metabolic labeling to analyze regulation space...
A key goal of developmental biology is to understand how a single cell transforms into full-grown organism consisting many cells. Although impressive progress has been made in lineage tracing using imaging approaches, analysis vertebrate trees mostly limited relatively small subsets Here we present scartrace, strategy for massively parallel clonal based on Cas9 induced genetic scars the zebrafish.
Simultaneous profiling of single-cell gene expression and lineage history holds enormous potential for studying cellular decision-making. Recent computational approaches combine both modalities into trajectories; however, they cannot make use all available information in destructive time-series experiments. Here, we present moslin, a Gromov-Wasserstein-based model to couple profiles across time points based on information. We validate our approach simulations demonstrate Caenorhabditis...
Extrachromosomal DNA (ecDNA) is a common source of oncogene amplification across many types cancer. The non-Mendelian inheritance ecDNA contributes to heterogeneous tumour genomes that rapidly evolve resist treatment. Here, using single-cell and live-cell imaging, single-micronucleus sequencing, computational modelling, we demonstrate elevated levels predisposes cells micronucleation. Damage on ecDNA, commonly arising from replication stress, detaches the chromosomes upon which they...
Abstract Simultaneous profiling of single-cell gene expression and lineage history holds enormous potential for studying cellular decision-making beyond simpler pseudotime-based approaches. However, it is currently unclear how information across experimental time points can be combined in destructive experiments, which particularly challenging in-vivo systems. Here we present moslin, a Fused Gromov-Wasserstein-based model to couple matching profiles points. In contrast existing methods,...
We study compactifications of type IIA supergravity on six-dimensional manifolds with SU(2) structure and compute the low-energy effective action in terms non-trivial intrinsic torsion. The consistency gauged $ \mathcal{N} = 4 is established gauge group determined. Depending torsion, antisymmetric tensor fields can become massive.
A key goal of developmental biology is to understand how a single cell transforms into full-grown organism consisting many different types. Single-cell RNA-sequencing (scRNA-seq) has become widely-used method due its ability identify all types in tissue or organ systematic manner 1–3 . However, major challenge organize the resulting taxonomy lineage trees revealing origin cells. Here, we present strategy for simultaneous tracing and transcriptome profiling thousands By combining scRNA-seq...
Abstract With the exception of lamina-associated domains, radial organization chromatin in mammalian cells remains largely unexplored. Here, we describe genomic loci positioning by sequencing (GPSeq), a genome-wide method for inferring distances to nuclear lamina all along radius that works gradual enzymatic restriction from towards nucleus center, followed generated cut sites. Using GPSeq, mapped human genome at 100 kb resolution, which revealed patterns and epigenomic features, gene...
Myocardial infarction is a leading cause of death worldwide, as the adult human heart does not have ability to regenerate efficiently after insults. In contrast, zebrafish has high capacity for regeneration, and understanding mechanisms regenerative processes in fish allows identification novel therapeutic strategies. While several pro-regenerative factors been described, cell types orchestrating regeneration remain largely elusive. To overcome this conceptual limitation, we dissected type...