Chongyuan Luo

Epigenomic heterogeneity and spatial organization during human reprogramming

This study examines epigenomic and spatial changes during human reprogramming, finding distinct molecular and spatial patterns in productive versus unsuccessful trajectories.

map3C: a computational tool for processing multiomic single-cell Hi-C data

map3C improves the quality of multiomic single-cell Hi-C data and aids in identifying structural variant locations.

Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation

The paper maps 3D genome organization and DNA methylation across 86,689 single nuclei from 16 human tissues, revealing cell-type-specific variations and discrepancies between methylation and chromatin structure.

Spatial and Molecular Progression of Neural Progenitor Cells in the Developing Human Dentate Gyrus

This study maps the spatial and molecular changes in neural progenitor cells in the human dentate gyrus from gestation to postnatal stages, showing a decline in neurogenic potential and transition to astrocytic features.

Distinct cellular DNA methylation mechanisms underlie common and rare genetic risk for brain disorders

The paper identifies distinct DNA methylation mechanisms for common and rare noncoding genetic risk in brain disorders using deep learning and single-nucleus DNAm data.

A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons

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.

An antagonistic epigenetic mechanism regulating gene expression in pollen revealed through single-nucleus multiomics

The paper reveals an antagonistic epigenetic mechanism in Arabidopsis pollen where MBD5/6 repress methylated loci while MBD7 promotes demethylation and transcriptional activation.

Integrated ambient modeling and genetic demultiplexing of single-cell RNA+ATAC multiome experiments with Ambimux

The paper introduces ambimux, a method to estimate and demultiplex ambient molecule contamination in single-cell RNA+ATAC multiome data, improving the detection of biologically meaningful signals.

Single-cell DNA methylome and 3D genome atlas of the human subcutaneous adipose tissue

The paper characterizes the epigenomic and 3D genomic landscape of human subcutaneous adipose tissue at the cell-type level and links epigenomic variation to abdominal obesity risk.

A Single-Cell Atlas of DNA Methylation in Autism Spectrum Disorder Reveals Distinct Regulatory and Aging Signatures

The paper presents a single-cell DNA methylation and transcriptomics analysis of ASD, identifying cell type-specific methylation changes and age-related effects in the brain.

Integration of polygenic risk with single cell methylation profiles for depression

The paper integrates polygenic risk scores with single-cell methylation data to identify methylation-driven disease relevance in depression and other traits.

The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments

The paper evaluates demultiplexing methods for joint snRNA/snATAC experiments under ambient contamination and introduces a new metric to assess their performance.

Cell type-specific effects of age and sex on human cortical neurons

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.

scMeFormer: a transformer-based deep learning model for imputing DNA methylation states in single cells enhances the detection of epigenetic alterations in schizophrenia

Complementation testing identifies causal genes at quantitative trait loci underlying fear related behavior

The paper identifies causal genes at QTLs associated with fear-related behavior using complementation testing and finds six genes, including four with known synaptic roles and one long non-coding RNA.

Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain

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.

Epigenome erosion in Alzheimer's disease brain cells and induced neurons

This study identifies AD-specific DNA methylation signatures and chromosomal epigenome erosion in LOAD brain cells and shows their conservation in induced neurons.

Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes

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

Epigenomic and chromosomal architectural reconfiguration in developing human frontal cortex and hippocampus

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.

Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and is partly compensated by repressive histone modification H3K27me3

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

Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants

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.

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.

DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution

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

Rapid cost-effective viral genome sequencing by V-seq

The paper introduces V-seq, a cost-effective method for viral genome sequencing that uses multiplexed RT primers to improve coverage and reduce costs.

Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus

The paper maps DNA methylation changes across 12 mouse tissues at 8 developmental stages, identifying methylation variant regions and tissue-specific enhancers linked to human genetic diseases.

Loss of Dnmt3a dependent methylation in inhibitory neurons impairs neural function through a mechanism that impacts Rett syndrome

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.

Iterative Refinement of Cellular Identity from Single-Cell Data Using Online Learning

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.

Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons

This study examines DNA methylation changes during fibroblast-to-neuron reprogramming, identifying key factors and mechanisms involved in epigenomic remodeling.

Single-cell multi-omic profiling of chromatin conformation and DNA methylome

The paper develops sn-m3C-seq to profile chromatin conformation and DNA methylation in single nuclei, enabling high-resolution cell-type classification and chromatin map reconstruction in mice.