A5050006952- Single-cell and spatial transcriptomics
- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Immune Cell Function and Interaction
- Genetic Associations and Epidemiology
- Gene expression and cancer classification
- Cancer Genomics and Diagnostics
- RNA Research and Splicing
- T-cell and B-cell Immunology
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Genetic and phenotypic traits in livestock
- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Genomic variations and chromosomal abnormalities
- Bioinformatics and Genomic Networks
- Immune cells in cancer
- Genetic diversity and population structure
- Genomics and Rare Diseases
- Forensic and Genetic Research
- Race, Genetics, and Society
- RNA modifications and cancer
- Extracellular vesicles in disease
- Mesenchymal stem cell research
- Cell Image Analysis Techniques
University of Chinese Academy of Sciences
2023-2025
Shanghai Institute of Nutrition and Health
2023-2025
Chinese Academy of Sciences
2009-2024
Southern University of Science and Technology
2017-2024
Jiangsu University
2024
Southwest University of Science and Technology
2019-2020
National Heart Lung and Blood Institute
2013-2018
National Institutes of Health
2015-2017
Center for Systems Biology
2017
Shanghai Institutes for Biological Sciences
2009-2015
To date, most genome-wide association studies (GWAS) and of fine-scale population structure have been conducted primarily on Europeans. Han Chinese, the largest ethnic group in world, composing 20% entire global human population, is largely underrepresented such studies. A well-recognized challenge fact that can cause spurious associations GWAS. In this study, we examined substructures a diverse set over 1700 Chinese samples collected from 26 regions across China, each genotyped at ∼160K...
Genetic studies of Tibetans, an ethnic group with a long-lasting presence on the Tibetan Plateau which is known as highest plateau in world, may offer unique opportunity to understand biological adaptations human beings high-altitude environments. We conducted genome-wide study 1,000,000 genetic variants 46 Tibetans (TBN) and 92 Han Chinese (HAN) for identifying signals (HAAs) genomes. discovered most differentiated between TBN HAN at chromosome 1q42.2 2p21. EGLN1 (or HIFPH2, MIM 606425)...
Nucleosomes are present throughout the genome and must be dynamically regulated to accommodate binding of transcription factors RNA polymerase machineries by various mechanisms. Despite development protocols techniques that have enabled us map nucleosome occupancy genome-wide, dynamic properties nucleosomes remain poorly understood, particularly in mammalian cells. The histone variant H3.3 is incorporated into chromatin independently DNA replication requires displacement existing for its...
Demographic change of human populations is one the central questions for delving into past beings. To identify major population expansions related to male lineages, we sequenced 78 East Asian Y chromosomes at 3.9 Mbp non-recombining region, discovered >4,000 new SNPs, and identified many clades. The relative divergence dates can be estimated much more precisely using a molecular clock. We found that all Paleolithic divergences were binary; however, three strong star-like Neolithic ∼6 kya...
It is particularly meaningful to investigate natural selection in African Americans (AfA) due the high mortality their ancestry has experienced history. In this study, we examined 491,526 autosomal single nucleotide polymorphisms (SNPs) genotyped 5210 individuals and conducted a genome-wide search for signals 1890 AfA. Several genomic regions showing an excess of or European ancestry, which were considered footprints since population admixture, detected based on commonly used approach....
Abstract Our recent studies demonstrate that the focal adhesion protein Kindlin-2 is critical for chondrogenesis and early skeletal development. Here, we show deleting from osteoblasts using 2.3-kb mouse Col1a1-Cre transgene minimally impacts bone mass in mice, but 10-kb Dmp1-Cre transgene, which targets osteocytes mature osteoblasts, results striking osteopenia mice. loss reduces osteoblastic population increases osteoclastic adipocytic populations microenvironment. upregulates sclerostin...
Abstract Classic T cell subsets are defined by a small set of surface markers, while single-cell RNA sequencing (scRNA-seq) clusters cells using genome-wide gene expression profiles. The relationship between scRNA-seq clustered populations (scCPops) and marker–defined classic remains unclear. In this article, we integrated six bead-enriched with 62,235 transcriptomes from human PBMCs them into nine scCPops. Bead-enriched CD4+/CD45RA+/CD25− naive CD8+/CD45RA+ were mainly their scCPop...
Abstract Dimensionality reduction is crucial for the visualization and interpretation of high-dimensional single-cell RNA sequencing (scRNA-seq) data. However, preserving topological structure among cells to low dimensional space remains a challenge. Here, we present graph autoencoder (scGAE), dimensionality method that preserves in scRNA-seq scGAE builds cell uses multitask-oriented preserve information feature data simultaneously. We further extended visualization, clustering, trajectory...
In vertebrates, the type 1 parathyroid hormone receptor (PTH1R) is a critical regulator of skeletal development and homeostasis; however, how it modulated incompletely understood. Here we report that deleting Kindlin-2 in osteoblastic cells using mouse 10-kb Dmp1-Cre largely neutralizes intermittent PTH-stimulated increasing bone volume fraction mineral density by impairing both osteoblast osteoclast formation murine adult bone. Single-cell profiling reveals loss increases proportion...
Abstract Single-cell RNA sequencing provides exciting opportunities to unbiasedly study hematopoiesis. However, our understanding of leukemogenesis was limited due the high individual differences. Integrated analyses hematopoiesis and potentially new insights. Here we analyzed ~200,000 single-cell transcriptomes bone marrow mononuclear cells (BMMCs) its subsets from 23 clinical samples. We constructed a comprehensive cell atlas as hematopoietic reference. developed counterpart composite...
ABSTRACT Type III interferons (IFNs) primarily act on epithelial cells and protect against virus infection of the mucosa, whereas type I IFNs more systemically. To date, it has been unknown which subtypes in upper airways, primary site for initial most respiratory viruses, rely IFN or antiviral protection. address this question, we performed a single-cell transcriptomics analysis IFN-mediated response focusing airways mice. This work identified nine distinct cell types derived from olfactory...
The rapid growth of single-cell and spatial omics has outpaced computational methods capable unifying these data into a cohesive framework for tissue atlas construction cross-sample analysis. A critical bottleneck lies in the inability existing tools to co-embed cells from diverse technologies-spanning transcriptomics, epigenomics, proteomics-into shared reference space while preserving architecture molecular specificity. Here, we present Garfield (Graph-based Contrastive Learning Enables...
The bone marrow microenvironment contains heterogeneous stromal cells, which are critical for remodeling and provide essential supportive roles hematopoietic functions. Although the diversity of PDGFRα+β+ mesenchymal stromal/stem cells (MSCs) get consensus, osteo-lineage (OLCs) that constitute developmental trajectory osteoblasts largely remain unclear. Here, we construct a comprehensive atlas cell via performing integrative single analyses 77 samples from 14 datasets. Besides previously...