A5101969897- Single-cell and spatial transcriptomics
- RNA modifications and cancer
- Advanced biosensing and bioanalysis techniques
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Cancer-related molecular mechanisms research
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- MicroRNA in disease regulation
- Cancer, Hypoxia, and Metabolism
- Bioinformatics and Genomic Networks
- CRISPR and Genetic Engineering
- Salivary Gland Disorders and Functions
- Biosensors and Analytical Detection
- Cancer Genomics and Diagnostics
- Bacteriophages and microbial interactions
- Gene Regulatory Network Analysis
- RNA Interference and Gene Delivery
- Ferroptosis and cancer prognosis
- Obstructive Sleep Apnea Research
- RNA regulation and disease
- Oral microbiology and periodontitis research
- Immune cells in cancer
- Cell Image Analysis Techniques
- interferon and immune responses
Fu Jen Catholic University
2025
Jiangxi University of Traditional Chinese Medicine
2024
Beijing Radiation Center
2018-2024
BGI Research
2024
Beijing Friendship Hospital
2024
Capital Medical University
2024
BGI Group (China)
2021-2024
Lanzhou Petrochemical Polytechnic
2024
Central South University
2023
Chengdu Institute of Biology
2013-2023
Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view current methodologies precludes their systematic application analyze relatively large three-dimensional mid- late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays in situ RNA capture create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied...
Iron homeostasis is essential for health; moreover, hepcidin-deficiency results in iron overload both hereditary hemochromatosis and iron-loading anemia. Here, we identified modulators by functionally screening hepcidin agonists using a library of 640 FDA-approved drugs human hepatic Huh7 cells. We validated the C57BL/6J mice mouse model (Hfe-/- mice). Our screen revealed that anti-rheumatoid arthritis drug auranofin (AUR) potently upregulates expression. Interestingly, found canonical...
Abstract We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow ( http://github.com/liulab-dfci/MAESTRO ) for the integrative analyses single-cell RNA-seq (scRNA-seq) ATAC-seq (scATAC-seq) data from multiple platforms. MAESTRO provides functions pre-processing, alignment, quality control, expression chromatin accessibility quantification, clustering, differential analysis, annotation. By modeling gene regulatory potential...
Elucidating the cellular organization of cerebral cortex is critical for understanding brain structure and function. Using large-scale single-nucleus RNA sequencing spatial transcriptomic analysis 143 macaque cortical regions, we obtained a comprehensive atlas 264 transcriptome-defined cell types mapped their distribution across entire cortex. We characterized layer region preferences glutamatergic, GABAergic, non-neuronal types, as well regional differences in cell-type composition...
Essential genes are those whose loss of function compromises organism viability or results in profound fitness. Recent gene-editing technologies have provided new opportunities to characterize essential genes. Here, we present an integrated analysis that comprehensively and systematically elucidates the genetic regulatory characteristics human First, found act as 'hubs' protein-protein interaction networks, chromatin structure epigenetic modification. Second, represent conserved biological...
microRNAs (miRNAs) have been a class of promising disease diagnostic biomarkers and therapeutic targets for their important biological functions. However, because the high homology, interference from precursors (pri-miRNA, pre-miRNA), as well limitations in current assay technologies, it poses demand challenge specific, efficient, economic miRNA method. Here, we propose new detection method based on label-free probe small organic dye with sequence dependence, realizing sequence-specific...
Single-cell RNA sequencing (scRNA-seq) technologies allow numerous opportunities for revealing novel and potentially unexpected biological discoveries. scRNA-seq clustering helps elucidate cell-to-cell heterogeneity uncover cell subgroups dynamics at the group level. Two important aspects of data analysis were introduced discussed in present review: relevant datasets analytical tools. In particular, we reviewed popular models including K-means clustering, hierarchical consensus so on. Seven...
Cells do not live in a vacuum, but milieu defined by cell–cell communication that can be measured via emerging high-resolution spatial transcriptomics approaches. However, analytical tools fully leverage such data for kinetic modeling remain lacking. Here we present Spateo ( aristoteleo/spateo-release ), general framework quantitative spatiotemporal of single-cell resolution transcriptomics. delivers novel methods digitizing layers/columns to identify spatially-polar genes, and develops...
Abstract Metabolic reprogramming, a hallmark of cancer, is closely associated with tumor development and progression. Changes in glycolysis play crucial role conferring radiation resistance to cells. How changes the status cancer cells still unclear. Here we revealed TAB182 regulating lactate production cellular response ionizing radiation. Irradiation can significantly stimulate protein, inhibiting increases radiosensitivity. Proteomic analysis indicated that influences several vital...
Single-cell chromatin accessibility sequencing (scCAS) has emerged as a valuable tool for interrogating and elucidating epigenomic heterogeneity gene regulation. However, scCAS data inherently suffers from limitations such high sparsity dimensionality, which pose significant challenges downstream analyses. Although several methods are proposed to enhance data, there still that hinder the effectiveness of these methods. Here, we propose scCASE, enhancement method based on non-negative matrix...
This study utilizes the danmaku on Bilibili platform as research subject to examine how their characteristics vary according nature or focus of English teaching videos. By employing social network analysis, reveals distinctive features in danmaku. For videos categorized under linguistic knowledge (phonetics, vocabulary, and grammar), comments predominantly center around topics such phonetics, grammar. Conversely, language skills (listening, speaking, reading writing), primarily reflect a...
Abstract Global profile of gene expression at single-cell resolution remains to be determined for primates. Using a recently developed technology (“Stereo-seq”), we have obtained comprehensive spatial transcriptome map the whole-brain level cynomolgus monkeys, with ∼600 genes per cell 10 μm-thick coronal sections (up 15 cm 2 in size). Large-scale single-nucleus RNA-seq analysis ∼1 million cells helped identify types corresponding Stereo-seq profiles, providing 3-D type atlas monkey brain....
Abstract With the exponential growth of multi-omics data, its integration and utilization have brought unprecedented opportunities for interpretation gene regulation mechanisms comprehensive analyses biological systems. IAnimal (https://ianimal.pro/), a cross-species, knowledgebase, was developed to improve massive public data simplify information mine genetic objective traits. Currently, provides 61 191 individual omics genome (WGS), transcriptome (RNA-Seq), epigenome (ChIP-Seq, ATAC-Seq)...
Mitochondrion is an important organelle of eukaryotic cells and a critical target ionizing radiation (IR) outside the nucleus. The biological significance mechanism non-target effect originating from mitochondria have received much attention in field biology protection. In this study, we investigated effect, role, radioprotective cytosolic mitochondrial DNA (mtDNA) its associated cGAS signaling on hematopoietic injury induced by IR vitro culture vivo total body irradiated mice study. results...
Abstract The exploration of three-dimensional chromatin interaction and organization provides insight into mechanisms underlying gene regulation, cell differentiation disease development. Advances in chromosome conformation capture technologies, such as high-throughput (Hi-C) analysis by paired-end tag (ChIA-PET), have enabled the organization. However, high-resolution Hi-C ChIA-PET data are only available for a limited number lines, their acquisition is costly, time consuming, laborious...
SUMMARY Spatially resolved transcriptomic technologies are promising tools to study cell fate decisions in a physical microenvironment, which is fundamental for enhancing our knowledge of mammalian development. However, the imbalance between resolution, transcript capture and field view current methodologies precludes their systematic application analyze relatively large three-dimensional mid- late-gestation embryos. Here, we combined DNA nanoball (DNB) patterned arrays tissue RNA create...
Microorganisms contribute to the pathogenesis of obstructive sleep apnea (OSA)-associated hypertension (HTN), while more studies focus on intestinal microbiome. However, relationship between oral microbiota and OSA-associated HTN has yet be elucidated. This study aimed identify differences in salivary patients with OSA comorbid compared patients, furthermore evaluate microbiome changes increased blood pressure OSA.This collected samples from 103 participants, including 27 healthy controls,...
Abstract Background Epithelial-to-mesenchymal transition (EMT) is a critical event contributing to more aggressive phenotypes in cancer cells. EMT frequently activated radiation-targeted cells during the course of radiotherapy, which often endows cancers with acquired radioresistance. However, upstream molecules driving signaling pathways radiation-induced have not been fully delineated. Methods In this study, RNA-seq-based transcriptome analysis was performed identify early responsive genes...
Imaging and tracking tools for natural cellular RNA with improved biocompatibility, specificity, sensitivity are critical to understanding function providing insights into disease therapeutics. We developed a new genetically encoded sensor using fluorogenic allosteric aptamer (FaApt) the sensitive imaging of localization dynamics targets in live cells. Target RNAs can be specifically recognized our by forming perfectly complementary duplexes, which turn induce structural changes refold...