A5100455714- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- Gene Regulatory Network Analysis
- Immune cells in cancer
- Genetic Mapping and Diversity in Plants and Animals
- Chromosomal and Genetic Variations
- Forensic and Genetic Research
- Bioinformatics and Genomic Networks
- Cell Image Analysis Techniques
- Genomics and Rare Diseases
- Genetic diversity and population structure
- RNA modifications and cancer
- Genetic Associations and Epidemiology
- Plant and Fungal Species Descriptions
- Genomic variations and chromosomal abnormalities
- Cancer Genomics and Diagnostics
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- RNA and protein synthesis mechanisms
- Microbial Community Ecology and Physiology
- Time Series Analysis and Forecasting
- Domain Adaptation and Few-Shot Learning
- Hydrological Forecasting Using AI
Fudan University
2012-2024
Sun Yat-sen University
2018-2024
Nanchang Institute of Science & Technology
2024
Sichuan Agricultural University
2024
Aarhus University
2021-2023
West China Medical Center of Sichuan University
2020-2023
Huazhong Agricultural University
2014-2023
Chinese Academy of Sciences
2023
Northwest A&F University
2021-2023
Pudong Medical Center
2023
The gene numbers and evolutionary rates of birds were assumed to be much lower than those mammals, which is in sharp contrast the huge species number morphological diversity birds. It is, therefore, necessary construct a complete avian genome analyze its evolution. We constructed chicken pan-genome from 20 de novo assembled genomes with high sequencing depth, identified 1,335 protein-coding genes 3,011 long noncoding RNAs not found GRCg6a. majority these novel detected across most...
Glioma is a lethal brain cancer and lacking effective therapies. Challenges include no therapeutic target, intra- intertumoral heterogeneity, inadequate drugs, an immunosuppressive microenvironment, etc. Deciphering the pathogenesis of gliomas finding out working mechanisms are urgent necessary for glioma treatment. Identification prognostic biomarkers targeting biomarker genes will be promising therapy.From our RNA-sequencing data oxidative phosphorylation (OXPHOS)-inhibition sensitive...
Abstract Spatial transcriptomics (ST) has become a powerful tool for exploring the spatial organization of gene expression in tissues. Imaging-based methods, though offering superior resolutions at single-cell level, are limited either number imaged genes or sensitivity detection. Existing approaches enhancing ST rely on similarity between cells and reference RNA sequencing (scRNA-seq) cells. In contrast, we introduce stDiff, which leverages relationships abundance scRNA-seq data to enhance...
Targeted next-generation sequencing (NGS) has been widely used as a cost-effective way to identify the genetic basis of human disorders. Copy number variations (CNVs) contribute significantly genomic variability, some which can lead disease. However, effective detection CNVs from targeted capture data remains challenging. Here we present SeqCNV, novel CNV calling method designed use NGS data. SeqCNV extracts read depth information and utilizes maximum penalized likelihood estimation (MPLE)...
Malic acid (MA) is an important flavor in fruits and acts as a mediator series of metabolic pathways. It to understand the factors affecting MA metabolism for fruit improvement MA-mediated biological processes. However, accumulation controlled by complex heredity environmental factors, making it difficult predict regulate MA. In this study, we carried out genome-wide association study (GWAS) on using eight milestone models with two-environment repeats. A associated SNP variations were...
The cohesin complex contributes to ribosome function, although the molecular mechanisms involved are unclear. Compromised function is associated with a class of diseases known as cohesinopathies. One cohesinopathy, Roberts syndrome (RBS), occurs when mutation reduces acetylation Smc3 subunit. Mutation acetyltransferase impaired rRNA production, biogenesis, and protein synthesis in yeast human cells. Cohesin binding ribosomal DNA (rDNA) evolutionarily conserved from bacteria We report that...
Rapid developments of single-cell RNA sequencing technologies allow study responses to external perturbations at individual cell level. However, in many cases, it is hard collect the perturbed cells, such as knowing response a type drug before actual medication patient. Prediction silicon could alleviate problem and save cost. Although several tools have been developed, their prediction accuracy leaves much room for improvement.In this article, we propose scPreGAN (Single-Cell data base on...
Heterosis is a phenomenon that hybrids show superior performance over their parents. The successful utilization of heterosis has greatly improved rice productivity, but the molecular basis remains largely unclear.Here, transcriptomes young panicles and leaves two widely grown two-line super hybrid varieties (Jing-Liang-You-Hua-Zhan (JLYHZ) Long-Liang-You-Hua-Zhan (LLYHZ)) parents were analyzed by RNA-seq. Transcriptome profiling revealed 1,778 ~ 9,404 differentially expressed genes (DEGs) in...
As global climate change intensifies, accurate weather forecasting has become increasingly important, affecting agriculture, energy management, environmental protection, and daily life. This study introduces a hybrid model combining Convolutional Neural Networks (CNNs) Long Short-Term Memory (LSTM) networks to predict historical temperature data. CNNs are utilized for spatial feature extraction, while LSTMs handle temporal dependencies, resulting in significantly improved prediction accuracy...
Thirty-seven normal and primary open angle glaucoma (POAG) subjects were noninvasively imaged by a tailor-made real-time anterior segment swept source optical coherence tomography (SS-OCT) to demonstrate the differences of Schlemm's canal (SC) between POAG eyes. After cross-section images chamber acquired SS-OCT, SC was confirmed two independent masked observers average area, long diameter, perimeter measured. In circumference, diameter is 580.34±87.81 μm, 8023.89±1486.10 μm2, 272.83±49.39...
Abstract Frizzled 3 ( FZD3 ) gene is located on chromosome 8p21, a region that has been implicated in schizophrenia genetic linkage studies. The transmembrane receptor required for Wnt signal transduction cascades have thought to be involved producing the cytoarchitectural defects observed schizophrenia. Previous work showed strong association between locus and family‐based study. To confirm this issue further, we investigated four single nucleotide polymorphisms (SNPs) by case‐control study...
With the development of modern sequencing technology, hundreds thousands single-cell RNA-sequencing (scRNA-seq) profiles allow to explore heterogeneity in cell level, but it faces challenges high dimensions and sparsity. Dimensionality reduction is essential for downstream analysis, such as clustering identify subpopulations. Usually, dimensionality follows unsupervised approach.In this paper, we introduce a semi-supervised method named scSemiAE, which based on an autoencoder model. It...
Abstract The systematic characterization of cellular heterogeneity among tissues and cell-type-specific regulation underlying complex phenotypes remains elusive in pigs. Within the Pig Genotype-Tissue Expression (PigGTEx) project, we present a single-cell transcriptome atlas adult pigs encompassing 229,268 high-quality nuclei from 19 tissues, annotated to 67 major cell types. Besides within across further characterize prominent tissue-specific features functions muscle, epithelial, immune...
The first complete genome sequence of a p-nitrophenol (PNP)-degrading bacterium is reported here. Pseudomonas putida DLL-E4, Gram-negative isolated from methyl-parathion-polluted soil, can utilize PNP as the sole carbon and nitrogen source. P. DLL-E4 has 6,484,062 bp circular chromosome that contains 5,894 genes, with G+C content 62.46%.
The rapid development of next-generation sequencing (NGS) technology has continuously been refreshing the throughput data. However, due to lack a smart tool that is both fast and accurate, analysis task for NGS data, especially those with low-coverage, remains challenging. We proposed decision-tree based variant calling algorithm. Experiments on set real data indicate our algorithm achieves high accuracy sensitivity SNVs indels shows good adaptability low-coverage In particular, obviously...
Background: Genetic factors are important in spermatogenesis and fertility maintenance, potentially significant biomarkers for the early detection of infertility. However, further understanding these biological processes is required. Methods: In present study, we sought to identify associated genes by reanalyzing separate studies from Gene Expression Omnibus datasets (GSE45885, GSE45887 GSE9210) validation (GSE4797, 145467, 108886, 6872). The differential were used limma package R language....