M. Margarita Behrens

This study shows that maternal immune activation disrupts DNA methylation and transcriptome of cortical excitatory neurons, delaying their maturation and affecting synapse-related genes.

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 uses single-cell epigenomics to study brain aging in mice, finding heterochromatin instability and transcription factor dysfunction across multiple brain regions and cell types.

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

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 describes a multi-institutional program for collecting neurotypical human brains to support multiomic brain cell atlas studies, highlighting challenges and opportunities for donor recruitment.

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

This paper creates a high-resolution spatial transcriptomic atlas of the human basal ganglia, identifying 60 cell types and their spatial organization across multiple nuclei.

The paper identifies cell type-specific aneuploidy in the adult mouse brain, finding a strong enrichment of chromosome 16 trisomy in non-neuronal cells.

The paper maps epigenetic and spatial transcriptomic changes in aging mouse brain using single-cell multi-omic data and develops deep-learning models to predict age-related gene expression changes.

The paper examines age and sex effects on human cortical neurons using multiomic data, finding age-related changes in gene expression and DNA methylation, and sex differences in gene expression and X-inactivation escape.

The paper generates a single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain, identifying methylation patterns and regulatory networks across cell types and brain regions.

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.

The paper identifies gene-CRE pairs in mouse brain cells by integrating single-cell transcriptomes and epigenomes, controlling for gene co-expression.

The paper links single-cell epigenomes and projection patterns of 33,034 mouse neurons to identify transcriptomic and epigenomic properties of projection cell types.

The paper analyzes gene regulatory programs in the neocortex of rodents and primates using single-cell multiomics, finding rapid evolution of cell type-specific gene expression and TE-driven cCREs.

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.

This study shows that Dnmt3a knockout in mouse excitatory neurons disrupts synapse maturation and working memory, with partial compensation by H3K27me3.

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.

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.

The paper identifies 491,818 candidate cis regulatory elements in adult mouse brain sub-types and links them to target genes and transcriptional regulators involved in various pathways.

The paper generates a multimodal cell census and atlas of the mammalian primary motor cortex, revealing a unified molecular genetic landscape and cross-species taxonomy of 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.

The paper constructs a DNA methylation atlas of the mouse brain at single-cell resolution, revealing epigenetic diversity and spatial organization of neuronal subtypes.

The paper links epigenomic properties of cortical projection neurons to their anatomical and projection patterns using single-nucleus DNA methylation sequencing in mice.

SnapATAC is a software package for analyzing scATAC-seq data, revealing regulatory elements and transcriptional regulators in mouse brain cells.

This study shows that loss of Dnmt3a or MeCP2 in inhibitory neurons leads to distinct but overlapping neurological and molecular effects, with mCH playing a key role in Rett Syndrome pathogenesis.

The paper develops an online learning algorithm for integrating large single-cell datasets, enabling efficient processing of millions of cells with reduced memory usage and allowing iterative refinement of cellular identity.

This paper introduces snmC-seq2, an improved single-cell DNA methylome profiling method that enhances read mapping, reduces artifacts, and increases throughput and coverage uniformity.