Rebecca D. Hodge

Iterative co-creation of harmonized human and non-human primate cellular and structural ontologies and 3D common coordinate frameworks for the basal ganglia

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.

A single-cell transcriptomic atlas of the periventricular proliferative zone in the late gestation fetal brain in the pigtail macaque

The paper constructs a single-cell RNA-Seq atlas of the periventricular proliferative zone in late-gestation pigtail macaque fetal brain, revealing cell states similar to human fetal brain.

Multiregional single-cell profiling reveals shared and specialized cellular vulnerability in Alzheimer's disease

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.

A Multimodal Single-Cell Epigenomic and 3D Genome Atlas of the Human Basal Ganglia

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.

Technical and biological sources of noise confound multiplexed enhancer AAV screening

The paper presents a barcoded multiplex strategy to screen enhancer AAVs using single-cell RNA sequencing and taxonomy mapping, but finds significant technical and biological noise complicates accurate expression pattern analysis.

Single-cell multiomic human brain atlas reveals regulatory drivers of cortical regionality

The paper uses multiomic single-cell and spatial data to identify gene regulatory networks and transcription factors driving cortical regionality in the human brain.

A consensus spinal cord cell type atlas across mouse, macaque, and human

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

Single-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia

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.

Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain

The paper creates a single-cell atlas of transcription and chromatin states in the human brain, identifying regulatory programs and linking them to neuropsychiatric disorders.

An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia

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

The Caudate Nucleus Exhibits Distinct Pathology and Cell Type-Specific Responses Across Alzheimer's Disease

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

Circuit specific specialization of human basal ganglia astrocytes

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

Cross-species consensus atlas of the primate basal ganglia

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.

A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia

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.

Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque

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.

Somatic cancer driver mutations are enriched and associated with inflammatory states in Alzheimer's disease microglia

The paper identifies somatic driver mutations in microglia of Alzheimer's disease brains, showing increased clonal expansion and inflammatory signatures.

Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the human hypothalamus

The paper uses single-cell genomics to reconstruct developmental trajectories of 170 neuronal subtypes in the human hypothalamus across development.

Transcriptomic cytoarchitecture reveals principles of human neocortex organization

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.

A comparative atlas of single-cell chromatin accessibility in the human brain

The paper constructs a single-cell chromatin accessibility atlas of the human brain, identifies cell-type-specific regulatory elements, and develops models to predict regulatory function of disease risk variants.

Comparative transcriptomics reveals human-specific cortical features

This study uses single nucleus transcriptomics to compare human and non-human primate cortical tissues, identifying human-specific gene expression patterns and their potential functional roles.

Transcriptomic diversity of cell types across the adult human brain

This study identifies 461 cell clusters and 3313 subclusters in the adult human brain using single-nucleus RNA sequencing, revealing regional diversity in neurons and astrocytes.

Signature morpho-electric properties of diverse GABAergic interneurons in the human neocortex

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.

Multi-modal characterization and simulation of human epileptic circuitry

This study characterizes and simulates changes in human hippocampal granule cells during epilepsy progression, identifying ion channel modifications that increase excitability.

Epigenomic complexity of the human brain revealed by single-cell DNA methylomes and 3D genome structures

The paper identifies 188 cell types in the human brain using single-cell DNA methylation and 3D genome data, and develops a tool to predict cell types based on methylation patterns.

Inter-individual variation in human cortical cell type abundance and expression

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.

Conserved coexpression at single cell resolution across primate brains

The paper uses single-cell expression data from five primates to identify conserved and divergent gene coexpression patterns in the middle temporal gyrus, revealing human-specific genes associated with brain disorders.

Adversarial domain translation networks for fast and accurate integration of large-scale atlas-level single-cell datasets

Portal integrates large-scale single-cell datasets efficiently and accurately by preserving biological variation across samples, platforms, and species.

Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants

The paper develops a multi-omic single-nucleus sequencing method and framework to analyze regulatory genome diversity in human cortical cells and link it to disease risk variants.

Scalable in situ single-cell profiling by electrophoretic capture of mRNA

This paper introduces EEL FISH, a method for spatial transcriptome profiling that improves throughput while maintaining single-cell resolution, applied to mouse and human tissues.

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

The paper compares cellular diversity in the primary motor cortex across human, marmoset, and mouse using single-nucleus transcriptomics and epigenomics, finding conserved cell types and species-specific adaptations.