Nathan R. Zemke

The paper performs single-cell multiomics analysis of the human retina to identify regulatory elements and develop predictors for non-coding risk variants.

This study examines age-related changes in the human hippocampus using multi-omics data, revealing cell-type loss and epigenetic reprogramming linked to cognitive decline.

This paper identifies Mysm1 mutations as the cause of meander tail mouse cerebellum malformation and links them to hematological and neurological defects.

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

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.

This paper presents a chromosome-level genome assembly and annotation for the degu, improving contiguity, completeness, and gene annotation compared to previous assemblies.

This study presents a single-cell multi-omic atlas of Alzheimer's disease brain regions, revealing region-specific epigenomic changes and altered cell states.

This paper identifies JUNB as a key driver of chronic brain vascular inflammation in CCM disease through multi-omic analysis of endothelial cell activation.

The paper evaluates computational methods for predicting cell type-specific enhancers in the mouse cortex using in vivo validation data and finds that open chromatin and sequence models improve prediction accuracy.

This study shows that reduced TBX5 dosage affects 3D chromatin organization in human cardiomyocytes, with cell-to-cell variation and partial protection by CTCF co-occupancy.

The paper maps chromatin interactions in mouse fetal tissues and links them to gene expression and disease risk variants in humans.

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.

SnapATAC2 is a fast, scalable dimensionality reduction tool for single-cell omics data that improves accuracy and efficiency in capturing cellular heterogeneity across multiple modalities.

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 investigates how promoter-specific histone H3 acetylation changes during CBP/p300 inhibition, revealing homeostatic maintenance of promoter H3K18/27ac and a role for BRD4 in regulating paused Pol2 release.