A5100446728- Metaheuristic Optimization Algorithms Research
- CRISPR and Genetic Engineering
- Advanced Image Processing Techniques
- Advanced Multi-Objective Optimization Algorithms
- Video Coding and Compression Technologies
- Advanced Vision and Imaging
- Artificial Immune Systems Applications
- Epigenetics and DNA Methylation
- Plant biochemistry and biosynthesis
- Advanced biosensing and bioanalysis techniques
- Mosquito-borne diseases and control
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Virus-based gene therapy research
- Evolutionary Algorithms and Applications
- Insect symbiosis and bacterial influences
- Advanced Computational Techniques and Applications
- Advanced Image Fusion Techniques
- Genetics, Aging, and Longevity in Model Organisms
- Viral Infectious Diseases and Gene Expression in Insects
- Cancer-related gene regulation
- Machine Learning in Bioinformatics
- Stability and Control of Uncertain Systems
- RNA Interference and Gene Delivery
- Plant Gene Expression Analysis
Shaoxing University
2025
Shanxi Medical University
2024
Henan Normal University
2023-2024
Qiqihar University
2024
Shanxi Academy of Medical Sciences
2024
Institute of Mechanics
2024
Chinese Academy of Sciences
2024
University of Chinese Academy of Sciences
2024
Zhengzhou University of Light Industry
2014-2023
Yangtze University
2016-2023
Background: Recent assays for individual-specific genome-wide DNA methylation profiles have enabled epigenome-wide association studies to identify specific CpG sites associated with a phenotype. Computational prediction of site-specific levels is important, but current approaches tackle average within genomic locus and are often limited regions. Results: We characterize patterns, show that correlation among decays rapidly, making predictions solely based on neighboring challenging. built...
Abstract Because of their small size, the recently developed CRISPR-Cas12f nucleases can be effectively packaged into adeno-associated viruses for gene therapy. However, a systematic evaluation editing outcomes is lacking. In this study, we apply high-throughput sequencing method to comprehensively assess efficiency, specificity, and safety four Cas12f proteins in parallel with that Cas9 two Cas12a at multiple genomic sites. achieve robust cleavage most tested sites mainly produce deletional...
Visualization of chromosomal dynamics is important for understanding many fundamental intra-nuclear processes. Efficient and reliable live-cell multicolor labeling loci can realize this goal. However, the current methods are constrained mainly by insufficient throughput, efficiency, flexibility as well photostability. Here we have developed a new approach to dual-color imaging based on modified single-guide RNA (sgRNA) CRISPR/Cas9 system. The modification sgRNA was optimized structure-guided...
Identifying protein subchloroplast localization in chloroplast organelle is very helpful for understanding the function of proteins. There have existed a few computational prediction methods localization. However, these existing works ignored proteins with multiple locations when constructing models, so that they can predict only one all this kind multilabel proteins.To address problem, through utilizing label-specific features and label correlations simultaneously, novel classifier was...
Efficient and precise genome editing is essential for clinical applications generating animal models, which requires engineered nucleases with high ability while low off-target activity. Here we present a high-throughput sequencing method, primer-extension-mediated (PEM-seq), to comprehensively assess both specificity of nucleases. We showed CRISPR/Cas9-generated breaks could lead chromosomal translocations large deletions by PEM-seq. also found that Cas9 nickase possessed lower activity...
Abstract CRISPR–Cas9 generates double-stranded DNA breaks (DSBs) to activate cellular repair pathways for genome editing. The of DSBs leads small insertions or deletions (indels) and other complex byproducts, including large chromosomal translocations. Indels are well understood disrupt target genes, while the deleterious byproducts remain elusive. We developed a new in silico analysis pipeline previously described primer-extension-mediated sequencing assay comprehensively characterize...
Abstract The mechanism underlying unwanted structural variations induced by CRISPR-Cas9 remains poorly understood, and no effective strategy is available to inhibit the generation of these byproducts. Here we find that a high level translocations dependent on repeated cleavage at Cas9-targeting sites. Therefore, employ in which Cas9 fused with optimized TREX2 generate Cas9TX, exo-endonuclease, prevents perfect DNA repair thereby avoids cleavage. In comparison CRISPR-Cas9, CRISPR-Cas9TX...
An artificial immune system inspired by the fundamental principle of vertebrate system, for solving constrained optimization problems, is proposed. The analogy between mechanism biological response and formulation drawn. Individuals in population are classified into feasible infeasible groups according to their constraint violations that closely match with two states, inactivated activated, B-cells response. Feasible group focuses on exploitation areas through clonal selection,...
Abstract A series of Cas9 variants have been developed to improve the editing fidelity or targeting range CRISPR–Cas9. Here, we employ a high-throughput sequencing approach primer-extension-mediated analyze efficiency, specificity and protospacer adjacent motif (PAM) compatibility dozen SpCas9 at multiple target sites in depth, our findings validate high broad these variants. With regard PAM-flexible variants, detect significantly increased levels off-target activity propose trade-off...
The repair products of double-stranded DNA breaks (DSBs) are crucial for investigating the mechanism underlying damage as well evaluating safety and efficiency gene-editing; however, a comprehensively quantitative assay remains to be established. Here, we describe step-by-step instructions primer extension-mediated sequencing (PEM-seq), followed by framework data processing statistical analysis. PEM-seq presents full spectrum outcomes both genome-editing-induced endogenous DSBs in mouse...
Spatial transcriptomics has emerged as an invaluable tool, helping to reveal molecular status within complex tissues. Nonetheless, these techniques have a crucial challenge: the absence of single-cell resolution, resulting in observation multiple cells each spatial spot. While reference-based deconvolution methods aimed solve challenge, their effectiveness is contingent upon quality and availability RNA (scRNA) datasets, which may not always be accessible or comprehensive. In response...
Measuring the success of sustainable urban development has been difficult in past. However, as this become more important past few years, paper develops an innovative capacity measurement model based on principal component analysis (PCA) and Grey TOPSIS methodology, which a significantly comprehensive measurement, reduces processing time calculation difficulty. First, PCA is used to extract main components that affect city’s capacity. Then, actual level measured using TOPSIS, from value then...
Tumor sample classification has long been an important task in cancer research. Classifying tumors into different subtypes greatly benefits therapeutic development and facilitates application of precision medicine on patients. In practice, solid tumor tissue samples obtained from clinical settings are always mixtures normal cells. Thus, the data these mixed signals. The 'tumor purity', or percentage cells sample, will bias clustering results if not properly accounted for.In this article, we...
This experiment was conducted to investigate the effects of mulberry leaf extract (MLE) on alleviating fatty liver hemorrhagic syndrome (FLHS) in laying hens. The 576 Jing Fen hens 56 weeks age with good health and similar weights (1.76 ± 0.17 kg) were randomly divided into 6 groups, 8 replicates each group 12 chickens replicate. lasted d. control fed a corn-soybean meal diet. FLHS high energy-low protein (HELP) diet, other four experimental groups HELP diets supplemented 0.04, 0.40, 0.80,...
The ornamental plant Camellia japonica is widely distributed worldwide and susceptible to various environmental stresses. WRKY transcription factor (TF) an important node of tolerance. However, TFs from C. have not been reported yet. In this study, 48 CjWRKYs, namely, CjWRKY1 CjWRKY48, were identified. Protein structure analysis revealed that CjWRKY proteins contain a highly conserved motif (WRKYGQK) two variant motifs (WRKYGKK WRKYGRK). Phylogenetic indicated the CjWRKYs can be divided into...