Alana A. Oyama

The paper introduces Seq-o-Matic, an open-source automated in situ sequencer that reduces hands-on time and improves sequencing consistency across tissue sections.

The paper maps gene expression and axonal projections of neurons in the mouse primary visual cortex to reveal how retinotopy and cell-type-specific collateralization organize visual-stream output.

The paper uses single-cell projection mapping in mice and marmosets to show that thalamocortical projections are spatially segregated in marmosets but follow a conserved gradient in both species.

This study uses single-nucleus RNA-seq, ATAC-seq, and Multiome to analyze Alzheimer's disease across multiple brain regions, revealing shared and region-specific cellular vulnerabilities.

This study uses multimodal Patch-seq data to show that gene expression gradients in mouse basal ganglia neurons correlate with spatial location, physiology, and morphology.

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 analyzes multi-modal Patch-seq data from macaque striatum to reveal morphoelectric diversity and functional specialization of neuronal cell types, highlighting primate-specific features and differences from rodents.

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 integrates multimodal data to characterize human neocortical glutamatergic neurons, revealing morphoelectric properties that distinguish transcriptomic subclasses and highlight species-specific differences.

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

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.

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