Bing Ren

SUMO2 Deletion Changes Chromatin Accessibility and Enhances Cytotoxic T Cell Activation and Tumor Infiltration

This study shows that deleting SUMO2 in CD8+ T cells enhances their activation, tumor infiltration, and anti-tumor effects by altering chromatin accessibility and gene expression.

A Measure of Transcriptional Dyscoordination for Quantifying Aging in Single Cells

This paper introduces a measure of transcriptional dyscoordination to quantify aging in single cells, showing it increases with age and is linked to cellular processes like senescence and genome instability.

Ex vivo glioblastoma migration phenotypes define clinical recurrence and tumor heterogeneity

This study identifies two migratory phenotypes in glioblastoma cells ex vivo, linking them to clinical recurrence and tumor heterogeneity.

Targeting CyclinD1-CDK6 to Mitigate Senescence-Driven Inflammation and Age-Associated Functional Decline

This study shows that targeting CCND1-CDK6 reduces DNA damage, inflammation, and age-related decline in mice by suppressing SASP and ISG expression.

Aging-induced hepatocyte CD44 drives IL6/STAT3 signaling and associates with impaired neighboring T cell function.

This study shows that aging-induced CD44 in hepatocytes activates the IL6/JAK/STAT3 pathway, leading to impaired T cell function in the liver.

Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina

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

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.

Epigenetic and 3D genome reprogramming during the aging of human hippocampus

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.

An Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain

The paper constructs an integrative single-cell epigenomic atlas of the adult mouse brain, mapping chromatin states and gene regulatory programs across 100 cell subclasses.

Single-cell analysis of chromatin accessibility and gene expression in Drosophila melanogaster embryos following hypoxia treatment

This study examines hypoxia's effects on Drosophila embryos by analyzing chromatin accessibility and gene expression, identifying dose-dependent changes and a critical role for the tramtrack gene in germ cell development.

A Multimodal Single-Cell Epigenomic and 3D Genome Atlas of the Human Basal Ganglia

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.

Correcting spatial transcriptomics data affected by a prevalent transcript leakage problem across platforms, species, and tissues

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.

A Community Standard Multispecies Cell Atlas of the Basal Ganglia

The paper presents a cross-species, multimodal atlas of the basal ganglia using single-cell transcriptomics and integrates epigenomic and spatial genomic data to enable cross-species comparisons.

Single-molecule spatial genomics reveals the multi-scale organization and plasticity of extrachromosomal DNA in glioblastoma

This study uses single-molecule spatial genomics to show how extrachromosomal DNA is organized and regulated in glioblastoma, linking it to tumor heterogeneity and microenvironmental influences.

Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging

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.

Single-cell multiomic human brain atlas reveals regulatory drivers of cortical regionality

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

Single-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia

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.

Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain

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.

An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia

The paper presents an integrated single-cell and epigenomic resource for exploring basal ganglia datasets across species, enabling multi-omics and comparative analysis.

Chromosome-level genome assembly and annotation of the degu (Octodon degus)

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

UC Irvine Brain Initiative Cell Atlas Network (BICAN) Brain Procurement Program for the Center for Multiomic Human Brain Cell Atlas Project

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.

An integrated view of the structure and function of the human 4D nucleome

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

Multiscale Spatial Transcriptomic Atlas of Human Basal Ganglia Cell-Type and Cellular Community Organization

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.

Brain Region-Specific Epigenomic Reorganization and Altered Cell States in Alzheimer's Disease

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

Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex

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.

Single cell multiomics reveals drivers of metabolic dysfunction-associated steatohepatitis

This study uses single-cell multi-omics to identify cell type-specific regulatory networks and novel therapeutic targets in MASLD.

Single cell multiomics and 3D genome architecture reveal novel pathways of human heart failure

The paper integrates single-cell multi-omics and 3D genome data from human hearts to identify gene regulatory changes and causal genetic contributors in heart failure.

Extensive folding variability between homologous chromosomes in mammalian cells

The paper uses GAM to study haplotype-specific 3D chromatin structures in mESCs, finding extensive allelic differences in chromatin architecture and gene expression mediated by Polycomb repression.

Cell-type-specific transposable element demethylation and TAD remodeling in the aging mouse brain

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.

Sensory Input, Sex, and Function Shape Hypothalamic Cell Type Development

The paper examines how sensory input, sex, and function influence the developmental trajectories of hypothalamic cell types during early life transitions.