Brian R. Herb

A comparative single-cell transcriptomic atlas for diverse populations of vertebrate hair cells

The paper constructs a cross-species single-cell transcriptomic atlas of hair cells across multiple vertebrates and identifies conserved and species-specific gene expression programs.

A consensus atlas of human brain development defines cell type-specific maturation trajectories across the lifespan

Reprocessing nine human brain datasets (2,157,582 cells, 156 donors, GW6 to adulthood) under one marker-based taxonomy yields 35 replicable cell types with cell type-specific timing of adult-like maturation.

STAPLE: automating spatial transcriptomics analysis and AI interpretation

STAPLE automates spatial transcriptomics analysis by integrating multiple tools into a modular framework and provides AI-driven interpretation of results.

A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development

The paper compiles a large transcriptomic dataset of neocortical development and uses joint matrix decomposition to identify conserved transcriptome dynamics across mammals and developmental stages.

Inhibition of autophagy-lysosomal function exacerbates microglial and monocyte lipid metabolism reprograming and dysfunction after brain injury

This study shows that inhibiting autophagy-lysosomal function worsens lipid metabolism reprogramming and dysfunction in microglia and monocytes after brain injury.

Leptin Activated Hypothalamic BNC2 Neurons Acutely Suppress Food Intake

The paper identifies BNC2 neurons in the hypothalamus that acutely suppress food intake by inhibiting AGRP neurons and are regulated by leptin, sensory cues, and nutritional status.

Transcriptional signatures of fentanyl use in the mouse ventral tegmental area

This study identifies transcriptional changes in mouse VTA cell types after fentanyl self-administration using single nuclei RNA sequencing.

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.

Cochlear organoids reveal epigenetic and transcriptional programs of postnatal hair cell differentiation from supporting cells

The paper identifies transcriptional and epigenetic programs driving hair cell differentiation from supporting cells in cochlear organoids and predicts novel regulatory factors.

Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data

The paper introduces MAMS, a metadata standard for single-cell data matrices and analysis workflows, to improve reproducibility and interoperability across datasets.

The Neuroscience Multi-Omic Archive: A BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain

The paper describes the Neuroscience Multi-Omic Archive, a repository for single-cell transcriptomic and epigenomic data from mammalian brains, providing tools for data access and analysis.

The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide

The paper provides a guide to the BRAIN Initiative Cell Census Network (BICCN) data ecosystem, its tools, and resources for analyzing brain cell types across species.

Early-childhood inflammation blunts the transcriptional maturation of cerebellar neurons

The paper examines how early-life inflammation affects cerebellar neuron maturation in children, finding transcriptomic changes in Purkinje and Golgi neurons linked to neurodevelopmental disorders.

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.

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

The paper creates a comprehensive atlas of mouse primary motor cortex cell types using integrated transcriptomic and epigenomic data from over 600,000 samples.

gEAR: gene Expression Analysis Resource portal for community-driven, multi-omic data exploration

gEAR provides a community-driven portal for multi-omic data visualization, analysis, and sharing across species and data types.

Single-nucleus RNA-seq reveals dysregulation of striatal cell identity due to Huntington’s disease mutations

This study uses single-nucleus RNA-seq to analyze striatal cell types in a Huntington’s disease mouse model, revealing dysregulated gene expression and cell identity loss across multiple cell types.

Biological insights from multi-omic analysis of 31 genomic risk loci for adult hearing difficulty

The paper identifies 31 new genomic risk loci for hearing difficulty using GWAS and multi-omic analysis, highlighting gene regulation in cochlear cells.