Eran A. Mukamel

The paper introduces distributed AI agents to analyze large-scale biological datasets, demonstrating their ability to rapidly extract insights and predict outcomes across a Perturb-seq atlas.

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 study examines the cell-type specific effects of opioid use disorder and HIV on the human brain, identifying changes in gene regulation, metabolism, and immune responses across different brain regions.

The paper measures 5-methyl-cytosine and 5-hydroxymethyl-cytosine in human neurons across the lifespan, showing dynamic changes in hmC linked to transcription, chromatin state, and sex-specific gene regulation.

This study creates a 3D multi-omic atlas of developing human basal ganglia and inhibitory neurons, revealing lineage-specific 3D genomic dynamics and regulatory programs associated with neuropsychiatric disease risk.

This study uses spatial transcriptomics to show that Alzheimer's disease disrupts circadian rhythms in specific brain regions before amyloid plaques form in a mouse model.

The paper presents a brain organoid atlas of 352 patient-derived iPSCs from neurodevelopmental disorders, showing disease-specific cellular defects in organoids.

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 reanalyzes a study on memory-related gene expression using appropriate statistical methods and finds no significant differentially expressed genes.

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 examines transcriptome and epigenome changes in C9orf72 repeat expansion-associated ALS and FTD, showing distinct gene expression patterns in different cell types and brain regions.

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

The paper investigates epigenomic and 3D chromatin conformation changes in human frontal cortex and hippocampus development using sn-m3C-seq, finding distinct chromatin conformations in neurons and glial cells and linking risk variants to regulatory regions.

The paper quantifies RNA editing in human brain cell types, identifies cell-specific editing sites, and discovers cis-editing quantitative trait loci linked to genetic regulation.

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.