Nelson Johansen

The paper describes the iterative creation of harmonized ontologies and 3D frameworks for the basal ganglia across human and non-human primates to enable cross-species comparisons of cellular and molecular data.

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.

This paper creates a multimodal single-cell atlas of the human basal ganglia, revealing epigenomic and 3D genome features across cell types and linking them to disease-associated genetic risk.

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.

This paper introduces a standards framework for integrating single-cell and spatial omics data into brain cell atlases, enabling interoperable and reusable knowledge-ready resources.

MapMyCells maps unlabeled single-cell datasets to reference brain taxonomies, enabling cross-study integration and reproducible cell-type annotation.

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.

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

This paper presents a single-cell multiome atlas of the human basal ganglia, linking chromatin states and transcriptomes to cell-type identity and disease-associated variants.

The paper presents an integrated single-cell and epigenomic resource for exploring basal ganglia datasets across species, enabling multi-omics and comparative analysis.

The paper defines major axes of human basal ganglia astrocyte specialization using a multimodal atlas and identifies enhancer code for targeted viral tools.

The paper creates a cross-species consensus atlas of primate basal ganglia cell types using multiomic data from human, macaque, and marmoset, identifying 61 conserved cell types and a novel hybrid medium spiny neuron type.

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 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 identifies enhancers for spinal motor neurons and develops AAV vectors to target these cells in rodents and macaques, enabling functional studies and potential therapeutic applications.

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 study creates an integrated multimodal cell atlas of Alzheimer's disease by analyzing single nuclei transcriptomes, epigenomes, and spatial coordinates across AD stages.

The paper identifies sex-specific transcriptomic changes in a mouse model of Rett syndrome, showing more differentially expressed genes in females and non-cell-autonomous effects.

The paper uses single nucleus RNA-sequencing to analyze human cortical areas, revealing cell type proportions and gene expression patterns that correlate with functional connectivity and areal specialization.

The paper uses viral labeling and Patch-seq to define morpho-electric properties of GABAergic interneurons in human neocortex, revealing functional insights and reclassifying some SST neurons into PVALB subclass.

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

The paper identifies subclass-specific genes associated with electrophysiological features in mouse interneurons and links cell adhesion molecules to schizophrenia risk.

The paper assesses inter-individual variation in human cortical cell types across 75 individuals, finding significant variation in abundance and gene expression, particularly in deep layer glutamatergic neurons.

scProjection maps multi-modal RNA measurements to scRNA-seq atlases to extract single cell gene expression profiles and improve spatial and multi-modal analysis.

The paper compares cell types in human and mouse cortex using single nucleus RNA-sequencing, finding conserved architecture with species-specific differences.

scAlign integrates scRNA-seq datasets and identifies rare cell populations, demonstrating its ability to detect a rare cell type associated with malaria transmission.