Brian Long

Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering

The paper introduces SACCELERATOR, a framework for spatially aware clustering that improves benchmarking by incorporating expert feedback and consensus analysis across diverse datasets.

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.

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.

2D, or not 2D? Investigating Vertical Signal Integrity of Tissue Slices

This paper introduces a tool to detect overlapping cells and segmentation errors in 3D spatial transcriptomics data.

SCALPEL: A pipeline for processing large-scale spatial transcriptomics data

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

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.

Spatial patterning of transcriptional and regulatory programs in the primate subcortex

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.

Exploring the correspondence between gene expressionand thalamic nuclei using the THALMANAC resource

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.

MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics

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

Integrated multimodal cell atlas of Alzheimer's disease

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

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

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.

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.

Morpho-electric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex

The paper identifies transcriptomic and morpho-electric diversity in human neocortical layer 1 interneurons, revealing greater subclass distinction compared to mouse.

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.

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.

Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex

The paper investigates target cell-specific synaptic dynamics between excitatory and inhibitory neurons in human neocortex, finding similarities to rodent studies.

Reference-based cell type matching of spatial transcriptomics data

This study evaluates six algorithms for cell type matching in spatial transcriptomics data and presents consensus strategies for improved analysis.

Conservation and divergence in cortical cellular organization between human and mouse revealed by single-cell transcriptome imaging

This study compares cellular organization and interactions in human and mouse cortex using single-cell transcriptome imaging, finding conserved laminar organization but divergent cell-cell interactions in humans.

Comprehensive in situ mapping of human cortical transcriptomic cell types

The paper spatially maps human cortical cell types using in situ sequencing and single-nucleus RNA-sequencing to create a first spatial atlas of human cortical cells.

Cell segmentation-free inference of cell types from in situ transcriptomics data

This paper introduces SSAM, a cell segmentation-free method for cell-type identification and tissue domain detection in in situ transcriptomics data, showing it detects known and discovers new cell types in mouse brain tissues.

Conserved cell types with divergent features between human and mouse cortex

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

Classification of electrophysiological and morphological types in mouse visual cortex

The paper classifies neurons in mouse visual cortex into 17 electrophysiological and 35 morphological types using unsupervised methods and links them to transcriptomic types.

Multimodal cell type correspondence by intersectional mFISH in intact tissues

The paper presents a method combining spatial transcriptomics with optogenetic mapping to resolve cell type characteristics in mouse cortex.

h-channels contribute to divergent electrophysiological properties of supragranular pyramidal neurons in human versus mouse cerebral cortex

The paper shows that h-channels contribute to differences in electrophysiological properties between human and mouse supragranular pyramidal neurons.

SmartScope2: Simultaneous Imaging and Reconstruction of Neuronal Morphology

SmartScope2 is an automated neuron reconstruction tool that reduces image data requirements and increases imaging speed for human and mouse cortical neurons.