Andreas Bueckle

Multiscale harmonization, semantic integration, and immersive exploration of single-cell data in support of novel biological insights

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.

Organism-scale annotation with Pan-human Azimuth

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

SenNet Portal: Build, Optimization and Usage

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

A MEF2C transcription factor network regulates proliferation of glomerular endothelial cells in diabetic kidney disease

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 Common Fund Data Ecosystem (CFDE)

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.

Cell type populations for 3D anatomical structures of the Human Reference Atlas

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

Exploring endothelial cell environments across organs in spatially resolved omics data

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

Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph for Linked Open Data

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.

Benchmarking single cell transcriptome matching methods for incremental growth of cell atlases

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.

Robust and generalizable segmentation of human functional tissue units

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

The HRA Organ Gallery Affords Immersive Superpowers for Building and Exploring the Human Reference Atlas with Virtual Reality

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

Specimen, Biological Structure, and Spatial Ontologies in Support of a Human Reference Atlas

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.

Tissue Registration and Exploration User Interfaces in support of a Human Reference Atlas

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.

Real-Time Spatial Registration for 3D Human Atlas

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