A5068659777- Constraint Satisfaction and Optimization
- Bioinformatics and Genomic Networks
- Complex Network Analysis Techniques
- AI-based Problem Solving and Planning
- Gene expression and cancer classification
- Data Management and Algorithms
- Plant Molecular Biology Research
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- MicroRNA in disease regulation
- Metaheuristic Optimization Algorithms Research
- Advanced Graph Neural Networks
- Cancer-related molecular mechanisms research
- Logic, Reasoning, and Knowledge
- Chromosomal and Genetic Variations
- Advanced Database Systems and Queries
- Formal Methods in Verification
- Gene Regulatory Network Analysis
- Genomics and Chromatin Dynamics
- Opinion Dynamics and Social Influence
- Vehicle Routing Optimization Methods
- Molecular Biology Techniques and Applications
- RNA Research and Splicing
- Plant Stress Responses and Tolerance
- Genetic Mapping and Diversity in Plants and Animals
Jinan University
2015-2025
Sichuan Agricultural University
2025
Ministry of Agriculture and Rural Affairs
2025
Hong Kong Polytechnic University
2022-2025
Bureau of Geology and Mineral Exploration and Development of Guizhou Province
2020-2024
Aerospace Information Research Institute
2024
Chinese Academy of Sciences
2024
Northwestern Polytechnical University
2020-2024
Clinical Trial Investigators
2024
Shunde Polytechnic
2024
Small RNA-guided gene silencing at the transcriptional and post-transcriptional levels has emerged as an important mode of regulation in plants animals. Thus far, conventional sequencing small RNA libraries from rice led to identification most conserved miRNAs. Deep is effective approach uncover rare lineage- and/or species-specific microRNAs (miRNAs) any organism. In order identify new miRNAs possibly abiotic-stress regulated RNAs rice, three were constructed control seedlings exposed...
MicroRNA (miRNA)-guided target RNA expression is vital for a wide variety of biological processes in eukaryotes. Currently, miRBase (version 13) lists 142 and 353 miRNAs from Arabidopsis rice (Oryza sativa), respectively. The integration diverse networks relies upon the confirmation their targets. In contrast with well-characterized miRNA targets that are cleaved Arabidopsis, only few such have been confirmed rice. To identify small rice, we applied ‘degradome sequencing’ approach, which...
MicroRNAs are short, noncoding RNAs that play important roles in post-transcriptional gene regulation. Although many functions of microRNAs plants and animals have been revealed recent years, the transcriptional mechanism microRNA genes is not well-understood. To elucidate regulation genes, we study characterize, a genome scale, promoters intergenic Caenorhabditis elegans, Homo sapiens, Arabidopsis thaliana, Oryza sativa. We show most known these four species same type as protein-coding...
Community detection, a fundamental task for network analysis, aims to partition into multiple sub-structures help reveal their latent functions. detection has been extensively studied in and broadly applied many real-world problems. Classical approaches community typically utilize probabilistic graphical models adopt variety of prior knowledge infer structures. As the problems that methods try solve data be analyzed become increasingly more sophisticated, new have also proposed developed,...
Abstract Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present draft genome sequences of wild ancestor domesticated variety cassava comparative analyses with partial inbred line. We identify 1,584 1,678 gene models specific varieties, respectively, discover heterozygosity millions single-nucleotide variations. Our reveal genes involved photosynthesis, starch accumulation...
Psoriasis is a chronic and complex inflammatory skin disease with lesions displaying dramatically altered mRNA expression profiles.However, much less known about the of small RNAs.Here, we describe comprehensive analysis normal psoriatic miRNAome next-generation sequencing in large patient cohort.We generated 6.7 3 10 8 RNA reads representing 717 284 putative novel microRNAs (miRNAs).We also observed widespread isomiRs miRNA * s derived from loci, low frequency editing skin.The processing...
Identification of modular or community structures a network is key to understanding the semantics and functions network. While many detection methods have been developed, which primarily explore topologies, they provide little semantic information communities discovered. Although are closely related, effort has made discover analyze these two essential properties together. By integrating topology on nodes, e.g., node attributes, we study problems inference their simultaneously. We propose...
MicroRNAs (miRNAs) are key regulators of gene expression in development and stress responses most eukaryotes. We globally profiled plant miRNAs response to infection bacterial pathogen Pseudomonas syringae pv. tomato (Pst). sequenced 13 small-RNA libraries constructed from Arabidopsis at 6 14 h post non-pathogenic, virulent avirulent strains Pst. identified 15, 27 20 miRNA families being differentially expressed upon Pst DC3000 hrcC, EV avrRpt2 infections, respectively. In particular, a...
Co-expression network-based approaches have become popular in analyzing microarray data, such as for detecting functional gene modules. However, co-expression networks are often constructed by ad hoc methods, and analyses not been shown to outperform the conventional cluster analyses, partially due lack of an unbiased evaluation metric.Here, we develop a general approach both genes samples data. Our consists simple but robust rank-based network construction method, parameter-free module...
Pseudoknots have generally been excluded from the prediction of RNA secondary structures due to its difficulty in modeling. Although, several dynamic programming algorithms exist for pseudoknots using thermodynamic approaches, they are neither reliable nor efficient. On other hand, comparative methods more reliable, but often done an ad hoc manner and require expert intervention. Maximum weighted matching, algorithm pseudoknot with analysis, suffers low-prediction accuracy many cases.Here we...
Community structure is an important property of complex networks. The automatic discovery such a fundamental task in many disciplines, including sociology, biology, engineering, and computer science. Recently, several community algorithms have been proposed based on the optimization modularity function (Q) . However, problem NP-hard existing approaches often suffer from prohibitively long running time or poor quality. Furthermore, it has recently pointed out that optimizing Q will resolution...
Abstract Background In eukaryotes, microRNAs (miRNAs) have emerged as critical regulators of gene expression. The Silkworm ( Bombyx mori L.) is one the most suitable lepidopteran insects for studying molecular aspects metamorphosis because its large size, availability mutants and genome sequence. Besides, this insect also has been amply studied from a physiological biochemical perspective. Deep sequencing small RNAs isolated different stages silkworm powerful tool not only measuring changes...
Motivation: A fundamental problem of computational genomics is identifying the genes that respond to certain endogenous cues and environmental stimuli. This can be referred as targeted gene finding. Since regulation mainly determined by binding transcription factors cis-regulatory DNA sequences, most existing annotation methods, which exploit conservation open reading frames, are not effective in finding targetgenes. Results: viable approach elements known responsible for target genes. Given...
MicroRNAs (miRNAs) and small-interfering RNAs (siRNAs) have emerged as important regulators of gene expression in higher eukaryotes. Recent studies indicate that genomes plants encode lineage-specific species-specific miRNAs addition to the well-conserved miRNAs. Leguminous are grown throughout world for food forage production. To date lack genomic sequence data has prevented systematic examination small leguminous plants. Medicago truncatula, a diploid plant with near-completely sequenced...
Arabidopsis microRNA (miRNA) genes (MIR) give rise to 20- 22-nt miRNAs that are generated predominantly by the type III endoribonuclease Dicer-like 1 (DCL1) but do not require any RNA-dependent RNA Polymerases (RDRs) or Polymerase IV (Pol IV). Here, we identify a novel class of non-conserved MIR two small species, species and 23- 27-nt at same site. Genetic analysis using pathway mutants reveals RNAs typical DCL1 associated with Argonaute (AGO1). In contrast, accumulation from...
Abstract Background Many eukaryotic genomes encode cis -natural antisense transcripts ( -NATs). Sense and may form double-stranded RNAs that are processed by the RNA interference machinery into small interfering (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila , yeasts. However, many questions remain regarding features biogenesis of nat-siRNAs. Results Through deep sequencing, we identified more than 17,000 unique siRNAs corresponding to -NATs from...
MicroRNAs (miRNAs), which originate from precursor transcripts with stem-loop structures, are essential gene expression regulators in eukaryotes. We report 19 miRNA precursors Arabidopsis that can yield multiple distinct miRNA-like RNAs addition to miRNAs and miRNA*s. These precursor-derived often arranged phase form duplexes an approximately two-nucleotide 3'-end overhang. Their production depends on the same biogenesis pathway as their sibling does not require RNA-dependent RNA polymerases...
Orchidaceae is the second largest family of flowering plants, which highly valued for its ornamental purposes and medicinal uses. Dendrobium officinale a special orchid species that can grow without seed vernalization. Because whole-genome sequence D. publicly available, this poised to become convenient research model evolutionary, developmental, genetic studies Orchidaceae. Despite these advantages, methods manipulation are poorly developed in officinale. In study, based on previously...