A5046721596- Cell Image Analysis Techniques
- Digital Imaging for Blood Diseases
- Single-cell and spatial transcriptomics
- Gene Regulatory Network Analysis
- AI in cancer detection
- Advanced Fluorescence Microscopy Techniques
- Erythrocyte Function and Pathophysiology
- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- COVID-19 diagnosis using AI
- Epigenetics and DNA Methylation
- Radiomics and Machine Learning in Medical Imaging
- CAR-T cell therapy research
- Zebrafish Biomedical Research Applications
- S100 Proteins and Annexins
- Gene expression and cancer classification
- Genomics and Chromatin Dynamics
- Image Processing Techniques and Applications
- Pluripotent Stem Cells Research
- Hematopoietic Stem Cell Transplantation
- Neurogenesis and neuroplasticity mechanisms
- Acute Myeloid Leukemia Research
- Protease and Inhibitor Mechanisms
- Cell Adhesion Molecules Research
- Microbial Metabolic Engineering and Bioproduction
Helmholtz Zentrum München
2016-2025
Technical University of Munich
2018-2025
Center for Environmental Health
2015-2025
Nationwide Children's Hospital
2025
German Cancer Research Center
2023
Deutschen Konsortium für Translationale Krebsforschung
2023
Institute of Bioinformatics and Systems Biology
2010-2021
Heidelberg Institute for Stem Cell Technology and Experimental Medicine
2021
Constructor University
2008
Technical University of Darmstadt
2005-2007
: Diffusion maps are a spectral method for non-linear dimension reduction and have recently been adapted the visualization of single-cell expression data. Here we present destiny, an efficient R implementation diffusion map algorithm. Our package includes specific noise model allowing missing censored values. In contrast to previous implementations, further nearest-neighbour approximation that allows processing hundreds thousands cells functionality projecting new data on existing maps. We...
Abstract Quantitative analysis of bioimaging data is often skewed by both shading in space and background variation time. We introduce BaSiC, an image correction method based on low-rank sparse decomposition which solves issues. In comparison to existing tools, BaSiC achieves high-accuracy with significantly fewer input images, works for diverse imaging conditions robust against artefacts. Moreover, it can correct temporal drift time-lapse microscopy thus improve continuous single-cell...
Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at individual and colony level. An intriguing yet little understood phenomenon is that social contact pathogen-exposed individuals reduces susceptibility previously naive nestmates this pathogen. We tested whether such immunisation in Lasius ants against entomopathogenic fungus Metarhizium anisopliae based on active upregulation immune system following an infectious or passive protection...
To understand biological processes, it is necessary to reveal the molecular heterogeneity of cells by gaining access location and interaction all biomolecules. Significant advances were achieved super-resolution microscopy, but such methods are still far from reaching multiplexing capacity proteomics. Here, we introduce secondary label-based unlimited multiplexed DNA-PAINT (SUM-PAINT), a high-throughput imaging method that capable achieving virtually at better than 15 nm resolution. Using...
The human bone marrow (BM) niche sustains hematopoiesis throughout life. We present a method for generating complex BM-like organoids (BMOs) from induced pluripotent stem cells (iPSCs). BMOs consist of key cell types that self-organize into spatially defined three-dimensional structures mimicking cellular, structural and molecular characteristics the hematopoietic microenvironment. Functional properties include presence an in vivo-like vascular network, multipotent mesenchymal...
Hematopoiesis is an ideal model system for stem cell biology with advanced experimental access. A systems view on the interactions of core transcription factors important understanding differentiation mechanisms and dynamics. In this manuscript, we construct a Boolean network to myeloid differentiation, specifically from common progenitors megakaryocytes, erythrocytes, granulocytes monocytes. By interpreting hematopoietic literature translating evidence into rules, implement binary dynamics...
Abstract Background In recent years, high-throughput microscopy has emerged as a powerful tool to analyze cellular dynamics in an unprecedentedly high resolved manner. The amount of data that is generated, for example long-term time-lapse experiments, requires automated methods processing and analysis. Available software frameworks are well suited fluorescence images, but they often do not perform on bright field image varies considerably between laboratories, setups, even single...
MicroRNA-mediated control of gene expression via translational inhibition has substantial impact on cellular regulatory mechanisms. About 37% mammalian microRNAs appear to be located within introns protein coding genes, linking their the promoter-driven regulation host gene. In our study we investigate this linkage towards a relationship beyond transcriptional co-regulation.Using measures based both annotation and experimental data, show that intronic tend support genes by target with...
Abstract Scars are more severe when the subcutaneous fascia beneath dermis is injured upon surgical or traumatic wounding. Here, we present a detailed analysis of cell mobilisation by using deep tissue intravital live imaging acute wounds, fibroblast lineage-specific transgenic mice, and skin-fascia explants (scar-like in dish – SCAD). We observe that injury triggers swarming-like collective migration fibroblasts progressively contracts skin form scars. Swarming exclusive to fibroblasts,...
Article26 September 2018Open Access Transparent process Metabolic regulation of pluripotency and germ cell fate through α-ketoglutarate Julia Tischler orcid.org/0000-0003-4665-4141 Wellcome Trust/Cancer Research UK Gurdon Institute, University Cambridge, Search for more papers by this author Wolfram H Gruhn John Reid MRC Biostatistics Unit, Cambridge Institute Public Health, Biomedical Campus, The Alan Turing British Library, London, Edward Allgeyer orcid.org/0000-0002-2187-4423 Florian...
The combination of directed migration and immunosuppressive shielding enables effective T cell therapy in solid tumors.
Quantitative large-scale cell microscopy is widely used in biological and medical research. Such experiments produce huge amounts of image data thus require automated analysis. However, detection outlines (cell segmentation) typically challenging due to, e.g. high densities, cell-to-cell variability low signal-to-noise ratios.Here, we evaluate accuracy speed various state-of-the-art approaches for segmentation light images using real synthetic data. The results vary between datasets show...
Chromatin states must be maintained during cell proliferation to uphold cellular identity and genome integrity. Inheritance of histone modifications is central in this process. However, the modification landscape challenged by incorporation new unmodified histones each cycle, principles governing heritability remain unclear. We take a quantitative computational modeling approach describe propagation H3K27 H3K36 methylation states. measure combinatorial patterns mass spectrometry on...
While the analysis of mitochondrial morphology has emerged as a key tool in study function, efficient quantification microscopy images presents challenging task and bottleneck for statistically robust conclusions. Here, we present Mitochondrial Segmentation Network (MitoSegNet), pretrained deep learning segmentation model that enables researchers to easily exploit power morphology. We tested performance MitoSegNet against three feature-based algorithms machine-learning Ilastik. outperformed...
Explainable AI is deemed essential for clinical applications as it allows rationalizing model predictions, helping to build trust between clinicians and automated decision support tools. We developed an inherently explainable the classification of acute myeloid leukemia subtypes from blood smears found that high-attention cells identified by coincide with those labeled diagnostically relevant human experts. Based on over 80,000 single white cell images digitized 129 patients diagnosed one...