Katy Börner

A free Meta Quest virtual reality app harmonizes CODEX, Visium, Xenium, volumetric immunofluorescence and electron microscopy data from 5 organs into 4 scale levels using the Human Reference Atlas.

The paper introduces an AI framework to automate the extraction of functional tissue unit properties from publications, supporting the construction of the Human Reference Atlas.

The paper introduces methods to scale up the Human Reference Atlas by aligning tissue datasets across reference systems and using millitomes for bulk registration.

Pan-human Azimuth maps diverse human cells into a unified hierarchical typology, enabling cross-tissue comparisons and spatial transcriptomic annotation.

The paper presents a benchmark for 3D blood vessel segmentation in human kidney phase-contrast tomography images using top-performing deep learning solutions from a global competition.

The paper introduces the SenNet Portal, a resource for senescent cell data and tools, and discusses its usage and future developments.

This study identifies a MEF2C transcription factor network that regulates endothelial cell proliferation in diabetic kidney disease and shows that SGLT2i treatment can reverse its dysregulation.

The paper describes the Common Fund Data Ecosystem (CFDE), which integrates NIH Common Fund data resources to enable discovery, analysis, and collaboration across heterogeneous datasets.

The paper quantifies cell type populations across 3D anatomical structures using single-cell transcriptomics and proteomics data from the Human Reference Atlas.

The paper presents tools to validate and simplify ontology term hierarchies for better usability in biomedical research.

The paper analyzes endothelial cell environments across organs using spatially resolved omics data and provides an interactive tool for visualizing cell distances and neighborhoods.

The paper introduces the Human Reference Atlas Knowledge Graph, a large-scale linked data resource for biological entities, and describes its construction, deployment, and usage.

The paper benchmarks seven computational tools for matching cell types across cell atlases, finding variations in accuracy and proposing a framework for incremental growth of cell atlases.

This paper describes the construction and usage of the Human Reference Atlas (HRA) v2.0, which integrates multiscale data across 36 organs and provides tools for analysis and visualization.

The paper introduces a comprehensive catalog of 22 functional tissue units (FTUs) in 10 healthy human organs, detailing their anatomy, vasculature, and cellular composition.

This paper introduces DeepCell Types, a language-informed vision model for spatial proteomics cell phenotyping that generalizes across diverse datasets and marker panels.

This paper compiles a dataset linking HRA digital objects to experts, publications, funding, and datasets to support systematic HRA construction and usage.

The paper uses ontologies to integrate clinical, pathological, and molecular kidney data for precision medicine analysis.

The paper describes a machine learning competition to develop automated image segmentation tools for anatomical structures across human organs, resulting in models that will be used in the Human Reference Atlas.

The paper evaluates five algorithms for segmenting functional tissue units in kidney and colon tissues using histological stains, comparing their accuracy and generalizability.

The paper introduces a VR application for exploring the Human Reference Atlas, enabling immersive 3D visualization of reference organs and linked datasets.

This paper introduces the Common Coordinate Framework Ontology (CCFO) v2.0.1 to integrate specimen, biological structure, and spatial data for the Human Reference Atlas, enabling interoperability and programmatic access.

The paper presents software tools and user interfaces for annotating and exploring tissue data in a human reference atlas, enabling data harmonization and public access.

This paper introduces a framework for real-time 3D tissue block registration in a human atlas, demonstrating its practicality and efficiency through experiments.