Publications by authors named "E M Quardokus"
The Human Reference Atlas (HRA) for the healthy, adult body is developed by a team of international, interdisciplinary experts across 20+ consortia. It provides standard terminologies and data structures for describing specimens, biological structures, and spatial positions of experimental datasets and ontology-linked reference anatomical structures (AS), cell types (CT), and biomarkers (B). We introduce the HRA Knowledge Graph (KG) as central data resource for HRA v2.
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- The use of well-structured ontologies and ontology-aware tools enhances data and analyses to be FAIR (Findable, Accessible, Interoperable, Reusable), supporting effective lexical searches and biologically meaningful annotation grouping.
- Researchers face challenges in adopting ontologies, primarily due to their complexity and the tendency to create simplified hierarchies that may misuse relationship types, leading to ineffective organization.
- A suite of validation tools is introduced to help users align their hierarchies with established ontology structures, providing graphical reports and tailored views for various atlases like the HuBMAP Human Reference Atlas and the Human Developmental Cell Atlas.
Article Synopsis
- Cellular senescence, once thought to only occur in tissue cultures, is now recognized as playing complex roles in various biological processes across multiple species, including humans.
- Traditional understanding of senescent cells primarily comes from lab studies, but these cells are rare in actual tissues, and fully developed cells can also show signs of senescence.
- The SenNet Biomarkers Working Group has created recommendations for identifying senescent cells in tissues, analyzing literature on markers in mice and humans, and discussing new methods for detection that will assist researchers in the field.
The lack of standardization in antibody validation remains a major contributor to irreproducibility of human research. To address this, we have applied a standardized approach to validate a panel of antibodies to identify 18 major cell types and 5 extracellular matrix compartments in the human kidney by immunofluorescence (IF) microscopy. We have used these to generate an organ mapping antibody panel for two-dimensional (2-D) and three-dimensional (3-D) cyclical IF (CyCIF) to provide a more detailed method for evaluating tissue segmentation and volumes using a larger panel of markers than would normally be possible using standard fluorescence microscopy.
View Article and Find Full Text PDFMultiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Advances in the field now allow high-parameter data collection (>60 targets); however, considerable expertise and capital are needed to construct the antibody panels employed by these methods. Organ mapping antibody panels are community-validated resources that save time and money, increase reproducibility, accelerate discovery and support the construction of a Human Reference Atlas.
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