Jonas Windhager
A5065666199- Single-cell and spatial transcriptomics
- Cell Image Analysis Techniques
- ICT Impact and Policies
- Marketing and Advertising Strategies
- Cancer Genomics and Diagnostics
- Gene expression and cancer classification
- Health, Environment, Cognitive Aging
- Advanced Fluorescence Microscopy Techniques
- Evolution and Genetic Dynamics
- Delphi Technique in Research
- Bioinformatics and Genomic Networks
- Genomics and Chromatin Dynamics
- Immune cells in cancer
- Cancer Cells and Metastasis
- Scientific Computing and Data Management
- Cancer Immunotherapy and Biomarkers
- Bacterial Genetics and Biotechnology
- DNA Repair Mechanisms
- HER2/EGFR in Cancer Research
- Genetics, Bioinformatics, and Biomedical Research
- Biomedical and Engineering Education
- Computational Drug Discovery Methods
- Advanced Biosensing Techniques and Applications
- Radiomics and Machine Learning in Medical Imaging
- RNA and protein synthesis mechanisms
ETH Zurich
2019-2025
University of Zurich
2019-2025
Science for Life Laboratory
2024
Uppsala University
2024
Life Science Zurich
2019-2021
Broad Institute
2021
Abstract A holistic understanding of tissue and organ structure function requires the detection molecular constituents in their original three-dimensional (3D) context. Imaging mass cytometry (IMC) enables simultaneous up to 40 antigens transcripts using metal-tagged antibodies but has so far been restricted two-dimensional imaging. Here we report development 3D IMC for multiplexed analysis at single-cell resolution demonstrate utility technology by human breast cancer samples. The resulting...
How cell-to-cell copy number alterations that underpin genomic instability
Simultaneous profiling of the spatial distributions multiple biological molecules at single-cell resolution has recently been enabled by development highly multiplexed imaging technologies. Extracting and analyzing biologically relevant information contained in complex data requires use a diverse set computational tools algorithms. Here, we report user-friendly, customizable, interoperable workflow for processing generated The steinbock framework supports image pre-processing, segmentation,...
The heterogeneity of breast cancer plays a major role in drug response and resistance has been extensively characterized at the genomic level. Here, single-cell mass cytometry (BCMC) panel is optimized to identify cell phenotypes their oncogenic signalling states biobank patient-derived tumour xenograft (PDTX) models representing diversity human cancer. BCMC identifies 13 cellular (11 2 murine), associated with both subtypes specific features. Pre-treatment phenotypic composition determinant...
One goal of precision medicine is to tailor effective treatments patients' specific molecular markers disease. Here, we used mass cytometry characterize the single-cell signaling landscapes 62 breast cancer cell lines and five from healthy tissue. We quantified 34 in each line upon stimulation by growth factor EGF presence or absence kinase inhibitors. These data—on more than 80 million single cells 4,000 conditions—were fit mechanistic network models that provide insight into how process...
Multiplexed imaging is increasingly used to study tissue architecture in health and disease. To investigate the cancer tumor microenvironment, typically either micro-arrays or small patient cohorts are collect process data. However, studies performed over course of years, collecting data from thousands samples rare require specialized workflows ensure sample throughput reproducibility for production processing. Here, we present two such multiplexed immunofluorescence mass cytometry tissues...
Summary: The Imaging and Molecular Annotation of Xenografts Tumors Cancer Grand Challenges team was set up with the objective developing “next generation” pathology cancer research by using a combination single-cell spatial omics tools to produce 3D molecularly annotated maps tumors. Its activities overlapped, in some cases catalyzed, revolution biology that saw new technologies being deployed investigate roles tumor heterogeneity micro-environment. See related article Stratton et al., p. 22...
<p>IMAXT Consortium Author List</p>
<div>Summary:<p>The Imaging and Molecular Annotation of Xenografts Tumors Cancer Grand Challenges team was set up with the objective developing “next generation” pathology cancer research by using a combination single-cell spatial omics tools to produce 3D molecularly annotated maps tumors. Its activities overlapped, in some cases catalyzed, revolution biology that saw new technologies being deployed investigate roles tumor heterogeneity micro-environment.</p><p><a...
<p>IMAXT Consortium Author List</p>
The 2024 OME-NGFF Workflows Hackathon, held at the BioVisionCenter University of Zurich, brought together an international group researchers and developers to develop ecosystem around open, scalable, FAIR bioimage file format OME-Zarr. Over five days, participants tackled key challenges in four main areas: (1) advancing OME-Zarr specification, (2) enabling workflow interoperability by integrating image processing tasks across multiple open-source frameworks, (3) expanding Java support for...
The 2024 OME-NGFF Workflows Hackathon, held at the BioVisionCenter University of Zurich, brought together an international group researchers and developers to develop ecosystem around open, scalable, FAIR bioimage file format OME-Zarr. Over five days, participants tackled key challenges in four main areas: (1) advancing OME-Zarr specification, (2) enabling workflow interoperability by integrating image processing tasks across multiple open-source frameworks, (3) expanding Java support for...
Imaging-based spatial transcriptomics techniques generate data in the form of points belonging to different mRNA classes. A crucial part analyzing involves identification regions with similar composition These biologically interesting can manifest at scales. For example, classes on a cellular scale corresponds cell types, whereas compositions millimeter correspond tissue-level structures. Traditional for identifying such often rely complementary data, as pre-segmented cells, or lengthy...
With the aim of producing a 3D representation tumors, imaging and molecular annotation xenografts tumors (IMAXT) uses large variety modalities in order to acquire tumor samples produce map every cell its host environment. volume data produced project, we developed automatic workflows analysis pipelines. We introduce research methodology where scientists connect cloud environment perform close are located, instead bringing their local computers. Here, present infrastructure, discuss unique...
ABSTRACT Although genetic and epigenetic abnormalities in breast cancer have been extensively studied, it remains difficult to identify those patients who will respond particular therapies. This is due part our lack of understanding how the variability cellular signaling affects drug sensitivity. Here, we used mass cytometry characterize single-cell landscapes 62 cell lines five from healthy tissue. We quantified 34 markers each line upon stimulation by growth factor EGF presence or absence...
Summary DNA replication, the basis of genetic information maintenance, is a remarkably robust yet highly stochastic process. We present computational model that incorporates experimental genome structures and protein mobility dynamics to mechanistically describe foundations replication. Analysis about 300,000 in silico profiles for fission yeast indicates number firing factors rate-limiting dominates completion time. Incorporating probabilistic activation binding, full-genome duplication was...
Abstract With the aim of producing a 3D representation tumours, IMAXT uses large variety modalities in order to acquire tumour samples and produce map every cell its host environment. volume data produced project we develop automatic workflows analysis pipelines introduce research methodology where scientists connect cloud environment perform close are located instead bringing their local computers. Here present infrastructure, discuss unique computational challenges describe chains...
Abstract Imaging-based spatial transcriptomics techniques generate image data that, once processed, results in a set of points with categorical labels for different mRNA species. A crucial part analyzing downstream involves the analysis these point patterns. Here, biologically interesting patterns can be explored at scales. Molecular on cellular level would correspond to cell types, whereas millimeter scale tissue-level structures. Often, clustering methods are employed identify and segment...
Abstract Highly multiplexed imaging technologies are increasingly applied in biomedical research to identify underlying patterns of disease. As part an IMI-funded project, the IMMUcan (Integrated immunoprofiling large adaptive cancer patients cohorts) consortium will generate single-cell resolved molecular profiles for thousands from hospitals across Europe. Patient tissues be profiled using two modalities, multispectral immunofluorescence (mIF) and Imaging Mass Cytometry (IMC), junction...