Marcus J. Hooper

3D-MAESTRO automates processing of large-scale volumetric brain microscopy data, enabling scalable and reproducible analysis of mouse brain structures.

The paper maps conserved cell type signatures in the adult mouse brainstem and spinal cord using multi-omics data, revealing shared and region-specific features.

The paper develops a cross-species enhancer-AAV toolkit for targeting specific cell types in the basal ganglia across species, validated in mouse and macaque.

The paper introduces THALMANAC, a resource for analyzing single-cell transcriptomic data of the thalamus, revealing gene expression patterns that support and refine thalamic nucleus parcellation.

The paper introduces ExA-SPIM, a microscope that enables high-resolution imaging of large tissue samples without sectioning, demonstrating its use on mouse brains and human white matter.

The paper evaluates computational methods for predicting cell type-specific enhancers in the mouse cortex using in vivo validation data and finds that open chromatin and sequence models improve prediction accuracy.

The paper presents an enhancer AAV toolbox for targeting and perturbing striatal cell types and circuits in mice, with validated specificity and cross-species applicability.

The paper develops a toolkit of transgenic mouse lines and enhancer AAVs for selective targeting of cortical cell populations using transcriptomic and epigenomic data.

This paper creates a high-resolution transcriptomic and spatial cell type atlas of the whole adult mouse brain, revealing spatial organization and transcription factor codes for cell types.

This study shows that STAT pathway activation limits Ascl1-mediated chromatin remodeling in Muller glia, reducing their ability to regenerate neurons in the adult mouse retina.