A5102937394- Gene expression and cancer classification
- Single-cell and spatial transcriptomics
- Aquaculture Nutrition and Growth
- Genetic Mapping and Diversity in Plants and Animals
- Animal Nutrition and Physiology
- Genetic Associations and Epidemiology
- Cancer Genomics and Diagnostics
- Molecular Biology Techniques and Applications
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- Neuroinflammation and Neurodegeneration Mechanisms
- RNA modifications and cancer
- Neurogenesis and neuroplasticity mechanisms
- Microbial Metabolites in Food Biotechnology
- Gene Regulatory Network Analysis
- Mitochondrial Function and Pathology
- Extracellular vesicles in disease
- Computational Drug Discovery Methods
- Helicobacter pylori-related gastroenterology studies
- Genetic and phenotypic traits in livestock
- Algal biology and biofuel production
- Bioinformatics and Genomic Networks
- Crustacean biology and ecology
- Adipokines, Inflammation, and Metabolic Diseases
- Genomics and Phylogenetic Studies
University of Chinese Academy of Sciences
2018-2025
BGI Group (China)
2014-2025
BGI Research
2023-2025
Cancer Hospital of Chinese Academy of Medical Sciences
2023
Zhejiang Cancer Hospital
2023
China National GeneBank
2019-2020
Huazhong University of Science and Technology
2018
Chinese University of Hong Kong, Shenzhen
2017-2018
Harbin Medical University
2011-2017
Fourth Affiliated Hospital of Harbin Medical University
2011-2017
Abstract Protein-Protein Interactions (PPIs) are fundamental means of functions and signalings in biological systems. The massive growth demand cost associated with experimental PPI studies calls for computational tools automated prediction understanding PPIs. Despite recent progress, silico methods remain inadequate modeling the natural hierarchy. Here we present a double-viewed hierarchical graph learning model, HIGH-PPI, to predict PPIs extrapolate molecular details involved. In this...
Abstract Microalgal Chlorella has been demonstrated to process wastewater efficiently from piggery industry, yet optimization through genetic engineering of such a bio-treatment is currently challenging, largely due the limited data and knowledge in genomics. In this study, we first investigated differential growth rates among three wastewater-processing strains: sorokiniana BD09, BD08 sp . Dachan, previously published UTEX 1602, showing us that BD09 maintains best tolerance synthetic...
In humans, obesity is associated with increased or decreased levels of serum biochemical indicators. However, the relationship not as well understood in chickens. Due to long-term intense selection for fast growth rate, modern broilers have problem excessive fat deposition, exhibiting metabolic changes. current study, Northeast Agricultural University broiler lines divergently selected abdominal content (NEAUHLF) were used identify differences parameters between 2 lines. A total 18...
The brain of the domestic pig (Sus scrofa domesticus) has drawn considerable attention due to its high similarities that humans. However, cellular compositions (PB) remain elusive. Here we investigated single-nucleus transcriptomic profiles five regions PB (frontal lobe, parietal temporal occipital and hypothalamus) identified 21 cell subpopulations. cross-species comparison mouse hypothalamus revealed shared specific gene expression patterns at single-cell resolution. Furthermore, types...
It is well recognized that batch effect in single-cell RNA sequencing (scRNA-seq) data remains a big challenge when integrating different datasets. Here, we proposed deepMNN, novel deep learning-based method to correct scRNA-seq data. We first searched mutual nearest neighbor (MNN) pairs across batches principal component analysis (PCA) subspace. Subsequently, correction network was constructed by stacking two residual blocks and further applied for the removal of effects. The loss function...
Abstract Background Identifying causative variants is crucial for the diagnosis of rare genetic diseases. Over past two decades, application genome sequencing technologies in field has significantly improved diagnostic outcomes. However, complexity data analysis and interpretation continues to limit efficiency accuracy these applications. Various genotype phenotype-driven filtering prioritization strategies are used generate a candidate list expert curation, with final report determined...
Gene regulation is a fundamental process that allows organisms to adapt their environment and increase complexity through the action of nucleic acid-binding proteins (NBPs), such as transcription factors (TFs), which regulate specific sets genes under distinct conditions. These regulatory interactions form transcriptional networks (TRNs), can be further broken down into sub-networks (TRSNs) centered around individual TFs. TRSNs are more stable practical for analysis, making them ideal...
Abstract INTRODUCTION Understanding molecular, neuroanatomical, and neurophysiological changes in cognitive decline is crucial for comprehending Alzheimer's disease (AD) progression facilitating objective staging early screening. METHODS We enrolled 277 participants employed a multimodal approach, integrating genomics, metagenomics, metabolomics, magnetic resonance imaging (MRI), electroencephalogram (EEG) to investigate the AD continuum, from subjective (SCD) through mild impairment (MCI)...
Purposes: We aimed to characterize the USH2A genotypic spectrum in a Chinese cohort and provide detailed genetic profile for patients with USH2A-IRD. Methods: designed retrospective study wherein total of 1,334 diagnosed IRD were included as cohort, namely 1,278 RP 56 USH patients, well other types IEDs healthy family members control cohort. The genotype-phenotype correlation all participants variant was evaluated. Results: Etiological mutations USH2A, most common cause USH, found 16.34% (n...
Characterization of the specific expression and chromatin profiles genes enables understanding how they contribute to tissue/organ development mechanisms leading diseases. Whilst number single-cell sequencing studies is increasing dramatically; however, data mining reanalysis remains challenging. Herein, we systematically curated up-to-date most comprehensive datasets originating from 2760 bulk samples over 5.1 million single-cells multiple developmental periods humans model organisms. With...
Body mass index and waist circumference are simple measures of obesity. However, they do not distinguish between visceral subcutaneous fat, or muscle, potentially leading to biased relationships individual body composition parameters adverse health outcomes. The purpose this study was develop validate prediction models for volumetric adipose muscle.Based on cross-sectional data 18,457, 18,260, 17,052 White adults from the UK Biobank, we developed sex-specific equations estimate tissue (VAT),...
Abstract Precision medicine depends on high-accuracy individual-level genotype data. However, the whole-genome sequencing (WGS) is still not suitable for gigantic studies due to budget constraints. It particularly important construct highly accurate haplotype reference panel imputation. In this study, we used 10 000 samples with medium-depth WGS a that named CKB panel. By imputing microarray datasets, it showed outperformed compared panels in terms of both number well-imputed variants and...
Abstract Background Decapods are an order of crustaceans which includes shrimps, crabs, lobsters and crayfish. They occur worldwide great scientific interest as well being ecological economic importance in fisheries aquaculture. However, our knowledge their biology mainly comes from the group is most closely related to – insects. Here we produce a de novo transcriptome database, crustacean annotated (CAT) spanning multiple tissues life stages seven crustaceans. Description A total 71...
Viral infectious diseases are a devastating and continuing threat to human animal health. Receptor binding is the key step for viral entry into host cells. Therefore, recognizing receptors fundamental understanding potential tissue tropism or range of these pathogens. The rapid advancement single-cell RNA sequencing (scRNA-seq) technology has paved way studying expression in different tissues species at resolution, resulting huge scRNA-seq datasets. However, effectively integrating sharing...
Abstract Purpose To expand the mutation spectrum of patients with familial exudative vitreoretinopathy (FEVR) disease. Participants 74 probands (53 families and 21 sporadic probands) disease their available family members ( n = 188) were recruited for sequencing. Methods Panel‐based targeted screening was performed on all subjects. Before sanger sequencing, variants LRP5 , NDP FZD4 TSPAN12 ZNF408 KIF11 RCBTB1 JAG1 CTNNA1 genes verified by a series bioinformatics tools genotype–phenotype...
The bromocresol green (BCG) and purple (BCP) assays often yield discordant serum albumin results. This study seeks to test the hypothesis that bias in results are influenced by concentration of globulin subtypes. concentrations albumin, α1-globulin, α2-globulin, β-globulin γ-globulin determined 197 human specimens total protein quantification electrophoresis, BCG BCP assays. influence globulins on measurement is validated with mixtures globulins. assay was directly proportional α1-globulin...
1. Excessive deposition of body fat, especially abdominal is detrimental in chickens and the prevention excessive fat accumulation an important problem. The aim this study was to identify blood biochemical indicators that could be used as criteria select lean Yellow-feathered chicken lines. 2. Levels fed fasted states traits were measured 332 Guangxi Yellow chickens. In state, genetic correlations (rg) triglycerides very low density lipoprotein levels positive for (0.47 ≤ rg 0.67), whereas...
Helicobacter pylori exhibit specific geographic distributions that are related to clinical outcomes. Despite the high infection rate of H. throughout world, genetic epidemiology surveillance still needs be improved. This study used single nucleotide polymorphisms (SNPs) profiling approach based on whole genome sequencing (WGS) facilitate genomic population analyses and encourage dissemination microbial genotyping strategies worldwide. A total number 1,211 public genomes were downloaded...
Small insertions and deletions (indels) are critical yet challenging genetic variations with significant clinical implications. However, the identification of pathogenic indels from neutral variants in contexts remains an understudied problem. Here, we developed INDELpred, a machine-learning-based predictive model for discerning benign indels. INDELpred was established based on key features, including allele frequency, indel length, function-based gene-based features. A set comprehensive...
Abstract A novel sampling design is proposed that optimizes the spatial configuration of sites and captures maximum intraurban variability in ambient air pollution with a minimum sample size. Unlike classical design, deterministic approach adopted redundancy site selection minimized by controlling for autocorrelation. The was tested implemented medium-sized midwestern city. analysis suggested 32 were adequate to capture more than 95% total variance airborne particulate 10 µm or less...
Eukaryotic nucleic acid binding protein database (ENPD, http://qinlab.sls.cuhk.edu.hk/ENPD/) is a library of proteins (NBPs) and their functional information. NBPs such as DNA (DBPs), RNA (RBPs), (DRBPs) are involved in every stage gene regulation through interactions with RNA. Due to the importance NBPs, was constructed based on manual curation newly developed pipeline utilizing both sequenced transcriptomes genomes. In total has recorded 2.8 million motifs from 662 NBP families 2423...
Crustacea, the second largest subphylum of Arthropoda, includes species major ecological and economic importance, such as crabs, lobsters, crayfishes, shrimps, barnacles. With rapid development crustacean aquaculture biodiversity loss, understanding gene regulatory mechanisms growth, reproduction, crustaceans is crucial to both conservation this group organisms. In these biological processes, transcription factors (TFs) play a vital role in regulating expression. However, are still largely...