A5043534100- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Bioinformatics and Genomic Networks
- Single-cell and spatial transcriptomics
- Immune cells in cancer
- RNA Research and Splicing
- Reproductive Biology and Fertility
- RNA modifications and cancer
- Allergic Rhinitis and Sensitization
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- CRISPR and Genetic Engineering
- Microbial bioremediation and biosurfactants
- Food Allergy and Anaphylaxis Research
- Cancer, Lipids, and Metabolism
- RNA and protein synthesis mechanisms
- Microbial Community Ecology and Physiology
- Cancer Genomics and Diagnostics
- Pesticide and Herbicide Environmental Studies
- Metal-Catalyzed Oxygenation Mechanisms
- Cancer Cells and Metastasis
- Antibiotics Pharmacokinetics and Efficacy
- Drug Transport and Resistance Mechanisms
- Forest Insect Ecology and Management
- Genetic Syndromes and Imprinting
Chinese University of Hong Kong
2014-2025
Chinese University of Hong Kong, Shenzhen
2024
Army Medical University
2023
China National Center for Biotechnology Development
2015-2020
Abstract ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds cell types, providing a universal annotation for genome interpretation. However, particular applications, it may be advantageous to use customized annotation. Here, we develop such custom by leveraging advanced assays, as eCLIP, Hi-C, whole-genome STARR-seq on number data-rich types. A key aspect this is comprehensive experimentally derived networks both transcription factors RNA-binding...
Lymph node metastasis is the common route of gastric cancer. However, until now, heterogeneities tumor cells and microenvironment in primary tumors (PT) metastatic lymph nodes (MLN) cancer (GC) remains uncharacterized. In our study, single cell RNA sequencing was performed on tissues from PT MLN Trajectory analysis function enrichment analyses were conducted to decode underlying mechanisms contributing LN Heterogeneous composition immune distinct intercellular interactions analyzed. Based...
G9a is a lysine methyltransferase that regulates epigenetic modifications, transcription, and genome organization. However, whether these properties are dependent on one another or represent distinct functions of remains unclear. In this study, we observe widespread DNA methylation loss in depleted catalytic mutant embryonic stem cells. Furthermore, define how chromatin accessibility, transcriptional silencing both catalytic-dependent -independent manners. Reactivated retrotransposons...
Despite the remarkable success and efficacy of immune checkpoint blockade (ICB) therapy such as anti-PD-L1 antibody in treating cancers, myeloid-derived suppressor cells (MDSCs) that lead to formation protumor immunosuppressive microenvironment are one major contributors ICB resistance. Therefore, inhibition MDSC accumulation function is critical for further enhancing therapeutic a majority cancer patients. Artemisinin (ART), most effective antimalarial drug with tumoricidal immunoregulatory...
Abstract Here we present STModule, a Bayesian method developed to identify tissue modules from spatially resolved transcriptomics that reveal spatial components and essential characteristics of tissues. STModule uncovers diverse expression signals in transcriptomic landscapes such as cancer, intraepithelial neoplasia, immune infiltration, outcome-related molecular features various cell types, which facilitate downstream analysis provide insights into tumor microenvironments, disease...
One of the most common cockroach types in urban areas, American (Periplaneta americana), has been reported to impose an increased risk allergies and asthma. Limited groups allergens (Per a 1-13) have identified this species due lack genome-related information.To expand allergen profile P. americana, genomic, transcriptomic, proteomic approaches were applied. With support high-quality genome assembled using nanopore, Illumina, Hi-C sequencing techniques, potential based on protein homology....
Large language models (LLMs) exhibit the emergent ability of few-shot in-context learning (ICL), allowing them to learn from demonstrations in simple prompts without task-specific training. However, applying ICL biological sequences for classification, especially computational immunology, remains underexplored. Here, we apply with 18 general-purpose LLMs across five families three antibody characterization scenarios, including predicting humanness, specificity, and isotype. We evaluate...
BACKGROUND: Vascular hyperpermeability is one of the hallmarks acute lung injury, contributing to excessive inflammation and respiratory failure. The PPARδ (peroxisome proliferator-activated receptor delta) an anti-inflammatory transcription factor, although its role in endothelial barrier function remains unclear. Here, we studied essential maintaining vascular integrity during investigated underlying mechanisms. METHODS: Endothelial cell (EC)–selective knockout mice (Ppard EC-KO )...
An aerobic, Gram-stain-negative, short rod-shaped, non-spore-forming, cyhalothrin-degrading bacterial strain, XZ2 T , was isolated from the surface water of Hanjiang River in Wuhan, China. Strain grew optimally at pH 6.0, 30 °C and absence NaCl. The G+C content total DNA 64.1 mol%. 16S rRNA gene sequence strain showed highest similarity to that Camelimonas lactis M 2040 (99.1 %), followed by abortus UK34/07-5 (95.9 %) Chelatococcus daeguensis K106 (95.3 %). major cellular fatty acids were C...
A Gram-stain-negative, aerobic, yellow-pigmented, rod-shaped bacterium, designated strain SC_3 T , was isolated from pesticide-contaminated soil sediment. The able to mineralize 2-phenoxybenzoic acid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that formed a monophyletic lineage in the genus Sphingobium and showed highest similarity type strains of abikonense (97.0 %), followed by lactosutens (96.8 %) cloacae (96.7 %). DNA–DNA relatedness between its closest phylogenetic...
Abstract Bioactive hydrogels have emerged as promising artificial niches for enhancing stem cell‐mediated tendon repair. However, a substantial knowledge gap remains regarding the optimal combination of niche features targeted cellular responses, which often leads to lengthy development cycles and uncontrolled healing outcomes. To address this critical gap, an innovative, data‐driven materiomics strategy is developed. This approach based on in‐house RNA‐seq data that integrates...
Tyrophagus putrescentiae, commonly referred to as the mould mite or cheese mite, is especially well-known a storage that causes human allergic diseases.1 However, it has fewer reported allergen groups compared house dust mites of Dermatophagoides genus in WHO/IUIS nomenclature database.2, 3 In this omics era, multiple genome-based approaches have been boosting our understanding medically important mites.4-6 Using allergens database reference genes, 37 (up group 42) were predicted genome T....
Abstract ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds cell types, providing a universal annotation for genome interpretation. However, particular applications, it may be advantageous to use customized annotation. Here, we develop such custom by leveraging advanced assays, as eCLIP, Hi-C, whole-genome STARR-seq on number data-rich types. A key aspect this is comprehensive experimentally derived networks both transcription factors RNA-binding...
Abstract The precision-recall curve (PRC) and the area under (AUPRC) are useful for quantifying classification performance. They commonly used in situations with imbalanced classes, such as cancer diagnosis cell type annotation. We evaluate 10 popular tools plotting PRC computing AUPRC, which were collectively more than 3000 published studies. find AUPRC values computed by rank classifiers differently some produce overly-optimistic results.