Yang Xie

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.

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.

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.

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.

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 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.

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.

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.

Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery

The paper investigates how chromatin architecture, mediated by histone modifiers and loop-extrusion machinery, influences gene regulation in mouse embryonic stem cells under different conditions.

Droplet Hi-C for Fast and Scalable Profiling of Chromatin Architecture in Single Cells

The paper introduces Droplet Hi-C, a method for single-cell chromatin conformation profiling, and demonstrates its application in analyzing gene regulatory programs and detecting genetic variations in cancer cells.

A comparative atlas of single-cell chromatin accessibility in the human brain

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.

Novel start codons introduce novel coding sequences in the human genomes

This study identifies polymorphic and fixed start-gain mutations in human genomes, showing their potential to alter gene function and contribute to disease.