Josh Nagra

SCALPEL processes large-scale spatial transcriptomics data with improved 3D segmentation, doublet detection, and spatial alignment, showing better performance than previous methods.

The paper creates a cross-species spinal cord cell type atlas integrating data from mouse, macaque, and human, identifying conserved and species-specific features.

The paper maps AD-related pathological changes in the caudate nucleus at cellular resolution, identifying distinct features and cell type-specific responses.

This paper creates a cross-species spatial transcriptomic atlas of the basal ganglia in human, rhesus macaque, and common marmoset, revealing conserved molecular organization and cell type-specific compartments.

The paper presents a spatially resolved transcriptomic and gene regulatory atlas of primate subcortical regions, revealing spatially tuned transcriptional and regulatory programs across cell types.

The paper introduces MerQuaCo, an open-source tool to automatically detect and quantify imperfections in spatial transcriptomics data, improving quality assessment.

The paper develops AAV-based genetic tools to specifically target astrocytes and oligodendrocytes across species, revealing functional roles in reward-dependent acetylcholine responses.