Quan Zhu

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 identifies a widespread transcript leakage issue in spatial transcriptomics and introduces DeLeakage, a Bayesian method that improves data cleaning and cell-type annotation.

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

PantheonOS introduces a multi-agent framework for automated genomics analysis, achieving super-human performance in batch correction and gene panel selection across diverse biological tasks.

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.

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

MERFISH+ enables high-resolution spatial multi-omics mapping of gene expression and chromatin organization in developing human hearts with subcellular resolution.

The paper creates a high-resolution multimodal lung atlas using single-nucleus RNA and chromatin data from 11 healthy adults, identifying 70 cell populations and 332,846 chromatin regions.

Bento enables subcellular analysis of spatial transcriptomics data by defining domains, annotating localization patterns, and quantifying gene colocalization, demonstrating its use on multiple datasets.

This paper demonstrates that transient suppression of PTBP1 in aged glial cells can re-activate neurogenesis in murine and human brains, generating new neurons through canonical pathways.

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.

This paper introduces a spatial genome aligner that reconstructs chromosome architectures from DNA-FISH data and identifies chromosome ploidies, revealing new insights into chromatin organization.

This study investigates how CTCF binding sites mediate transcriptional insulation in mouse embryonic stem cells, showing that insulation depends on CTCF site number, sequence context, and TAD boundary location.

The paper investigates chromatin architecture changes during human cardiomyocyte differentiation and identifies HERV-H retrotransposons as key regulators of TAD boundaries and gene regulation.