Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage

\ua9 The Author(s) 2025. The Human BioMolecular Atlas Program (HuBMAP) aims to construct a 3D Human Reference Atlas (HRA) of the healthy adult body. Experts from 20+ consortia collaborate to develop a Common Coordinate Framework (CCF), knowledge graphs and tools that describe the multiscale structure of the human body (from organs and tissues down to cells, genes and biomarkers) and to use the HRA to characterize changes that occur with aging, disease and other perturbations. HRA v.2.0 covers 4,499 unique anatomical structures, 1,195 cell types and 2,089 biomarkers (such as genes, proteins and lipids) from 33 ASCT+B tables and 65 3D Reference Objects linked to ontologies. New experimental data can be mapped into the HRA using (1) cell type annotation tools (for example, Azimuth), (2) validated antibody panels or (3) by registering tissue data spatially. This paper describes HRA user stories, terminology, data formats, ontology validation, unified analysis workflows, user interfaces, instructional materials, application programming interfaces, flexible hybrid cloud infrastructure and previews atlas usage applications

Adaptable microfluidic system for single-cell pathogen classification and antimicrobial susceptibility testing

Significance Drug-resistant pathogens are one of the major global health risks. However, conventional antimicrobial susceptibility testing (AST) approaches, which typically rely on overnight culture to isolate bacteria, require 3–5 days. Despite rapid pathogen identification techniques having been developed, the ability to rapidly determine bacteria susceptibility represents an unmet need in clinical microbiology. Existing rapid AST techniques are often designed based on a small panel of bacteria and the system neither provides information about the bacterial species nor distinguishes polymicrobial samples. By incorporating an adaptable microfluidic design, we demonstrate a phenotypic AST system that rapidly determines the existence of bacteria, classifies major classes of bacteria, detects polymicrobial samples, and identifies antimicrobial susceptibility directly from clinical samples at the single-cell level.</jats:p