A5100738088- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Genetics and Plant Breeding
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Wheat and Barley Genetics and Pathology
- Shape Memory Alloy Transformations
- Cancer, Lipids, and Metabolism
- MicroRNA in disease regulation
- Prostate Cancer Treatment and Research
- Peptidase Inhibition and Analysis
- Chromosomal and Genetic Variations
- Soybean genetics and cultivation
- Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- Plant Molecular Biology Research
- Synthesis and biological activity
- Extracellular vesicles in disease
- Advanced Neural Network Applications
- Microencapsulation and Drying Processes
- Advanced Biosensing Techniques and Applications
- Genomics, phytochemicals, and oxidative stress
- biodegradable polymer synthesis and properties
- Network Time Synchronization Technologies
- Genomic variations and chromosomal abnormalities
- Proteins in Food Systems
Jiangnan University
2023-2025
Ministry of Education of the People's Republic of China
2025
Qingdao University
2024
Affiliated Hospital of Qingdao University
2024
University of California, Riverside
2017-2024
Yingkou Institute of Technology
2024
Institute of Subtropical Agriculture
2024
Chinese Academy of Sciences
2024
Academy of State Administration of Grain
2024
Jiangsu Normal University
2023
Abstract Genome-wide association studies (GWAS) have been widely used in genetic dissection of complex traits. However, common methods are all based on a fixed-SNP-effect mixed linear model (MLM) and single marker analysis, such as efficient analysis (EMMA). These require Bonferroni correction for multiple tests, which often is too conservative when the number markers extremely large. To address this concern, we proposed random-SNP-effect MLM (RMLM) multi-locus RMLM (MRMLM) GWAS. The simply...
Abstract Motivation The large-scale multidimensional omics data in the Genomic Data Commons (GDC) provides opportunities to investigate crosstalk among different RNA species and their regulatory mechanisms cancers. Easy-to-use bioinformatics pipelines are needed facilitate such studies. Results We have developed a user-friendly R/Bioconductor package, named GDCRNATools, for downloading, organizing analyzing GDC with an emphasis on deciphering lncRNA-mRNA related competing endogenous RNAs...
MicroRNAs (miRNAs), which play critical roles in gene regulatory networks, have emerged as promising diagnostic and prognostic biomarkers for human cancer. In particular, circulating miRNAs that are secreted into circulation exist remarkably stable forms, enormous potential to be leveraged non-invasive early cancer detection. Novel user-friendly tools desperately needed facilitate data mining of the vast amount miRNA expression from The Cancer Genome Atlas (TCGA) large-scale profiling...
Abstract Background The lesser grain borer ( Rhyzopertha dominica ), a worldwide primary pest of stored grain, causes serious economic losses and threatens food safety. R. can respond to changes in temperature, especially the adaptability heat. In this study, transcriptome analysis exposed different temperatures was performed elucidate differences gene expression underling molecular mechanism. Results Isoform-sequencing generated 17,721,200 raw reads yielded 20,416 full-length transcripts. A...
Human endogenous retroviruses (HERVs) are derived from the infection and integration of exogenetic retroviruses. HERVs account for 8% human genome, majority solitary LTRs (solo-LTRs) due to homologous recombination. Multiple findings have showed that solo-LTRs could provide an enormous reservoir transcriptional regulatory sequences involved in diverse biological processes, especially carcinogenesis cancer development. The link between diseases still remains poorly understood. This review...
Abstract Flowering time and seed size are traits related to domestication. However, identification of domestication-related loci/genes controlling the in soybean is rarely reported. In this study, we identified a total 48 loci based on RAD-seq genotyping natural population comprising 286 accessions. Among these, four chromosome 12 additional two chromosomes 11 15 were associated with flowering 16 size. Of five genes three size, Glyma11g18720 , Glyma11g15480 Glyma15g35080 homologous...
Abstract Composite interval mapping (CIM) is the most widely-used method in linkage analysis. Its main feature ability to control genomic background effects via inclusion of co-factors its genetic model. However, result often depends on how are selected, especially for small-effect and linked quantitative trait loci (QTL). To address this issue, here we proposed a new under framework genome-wide association studies (GWAS). First, single-locus random-SNP-effect mixed linear model GWAS was...
Abstract This study investigated the effects of bacterial inoculants and enzyme-based silage cocktails on dynamics fermentation, microbiome, nutritional value silages produced from low-quality biomasses reed, rice, corn straw. A 90-day ensiling trial was performed using five distinct combinations six basal species ( Lactobacillus plantarum , buchneri Pediococcus pentosaceus Aspergillus niger Bacillus subtilis Candida utilis ) three enzymes (xylanase, β-mannanase, glucanase). Each type...
Understanding the genetic function of forage quality-related traits, including crude protein (CP), neutral detergent fiber (NDF), acid (ADF), hemicellulose (HC), and cellulose (CL) contents, is essential for identification quality genes selection effective molecular markers in sorghum. In this study, we genotyped 245 sorghum accessions by 85,585 single-nucleotide polymorphisms (SNPs) obtained phenotypic data from four environments. The SNPs were applied to multi-locus genome-wide association...
We present GSPMD, an automatic, compiler-based parallelization system for common machine learning computations. It allows users to write programs in the same way as a single device, then give hints through few annotations on how distribute tensors, based which GSPMD will parallelize computation. Its representation of partitioning is simple yet general, allowing it express different or mixed paradigms parallelism wide variety models. infers every operator limited user annotations, making...
Background Globally, gastric cancer (GC) is a category of prevalent malignant tumors. Its high occurrence and fatality rates represent severe threat to public health. According recent research, lipid metabolism (LM) reprogramming impacts immune cells’ ordinary function critical for the onset development cancer. Consequently, article conducted sophisticated bioinformatics analysis explore potential connection between LM GC. Methods We first undertook differential TCGA queue recognize...
Seed oils provide a renewable source of food, biofuel and industrial raw materials that is important for humans. Although many genes pathways acyl-lipid metabolism have been identified, little known about whether there specific mechanism high-oil content in plants. Based on the distinct differences seed oil between four dicots (20~50%) three low-oil grasses (<3%), comparative genome, transcriptome differential expression analyses were used to investigate this mechanism. Among 4,051...
HIGD1B (HIG1 Hypoxia Inducible Domain Family Member 1B) is a protein-coding gene linked to the occurrence and progression of various illnesses. However, its precise function in gastric cancer (GC) remains unclear.
Abstract Most TRIM family members characterized by the E3-ubiquitin ligases, participate in ubiquitination and tumorigenesis. While there is a dearth of comprehensive investigation for entire gastric cancer (GC). By combining TCGA GEO databases, common (TRIMs) were obtained to investigate gene expression, mutations, clinical prognosis. On basis TRIMs, consensus clustering analysis was conducted, risk assessment system prognostic model developed. Particularly, TRIM31 with diagnostic value...
Compared with genomic data of individual markers, haplotype provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational experimental phasing methods have been developed analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility this valuable genetic resource. Gamete cells, natural packaging haploid complements, are ideal materials entire chromosomes...
Abstract Prognostic tests using expression profiles of several dozen genes help provide treatment choices for prostate cancer (PCa). However, these require improvement to meet the clinical need resolving overtreatment, which continues be a pervasive problem in PCa management. Genomic selection (GS) methodology, utilizes whole-genome markers predict agronomic traits, was adopted this study prognosis. We leveraged The Cancer Genome Atlas (TCGA) database evaluate prediction performance six GS...