Bruce W. Herr

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

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

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.

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

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

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.