A5090322041- Plant Virus Research Studies
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- RNA modifications and cancer
- Machine Learning in Bioinformatics
- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- Viral gastroenteritis research and epidemiology
- Chromosomal and Genetic Variations
- Data Mining Algorithms and Applications
- Epigenetics and DNA Methylation
- Cancer-related molecular mechanisms research
- Rough Sets and Fuzzy Logic
- Text and Document Classification Technologies
- Animal Virus Infections Studies
- RNA and protein synthesis mechanisms
- Complex Network Analysis Techniques
- Technology and Security Systems
- AI-based Problem Solving and Planning
- Energy Efficient Wireless Sensor Networks
- Ginseng Biological Effects and Applications
- Advanced Measurement and Detection Methods
- Environmental DNA in Biodiversity Studies
- Distributed and Parallel Computing Systems
- Infrared Target Detection Methodologies
Central South University
2016-2025
Shanghai Zhangjiang Laboratory
2024
Changchun University of Technology
2023
Jiangnan University
2022
Yangtze University
2022
Carnegie Institution for Science
2022
Zhengzhou University
2022
Fuyang City People's Hospital
2022
Jiangxi University of Traditional Chinese Medicine
2020-2021
China University of Petroleum, Beijing
2016-2021
Abstract Motivation The Oxford Nanopore sequencing enables to directly detect methylation states of bases in DNA from reads without extra laboratory techniques. Novel computational methods are required improve the accuracy and robustness state prediction using reads. Results In this study, we develop DeepSignal, a deep learning method Testing on Homo sapiens (H. sapiens), Escherichia coli (E. coli) pUC19 shows that DeepSignal can achieve higher performance at both read level genome detecting...
Abstract In plants, cytosine DNA methylations (5mCs) can happen in three sequence contexts as CpG, CHG, and CHH (where H = A, C, or T), which play different roles the regulation of biological processes. Although long Nanopore reads are advantageous detection 5mCs comparing to short-read bisulfite sequencing, existing methods only detect CpG context, limits their application plants. Here, we develop DeepSignal-plant, a deep learning tool genome-wide all plants from reads. We Arabidopsis...
Long single-molecular sequencing technologies, such as PacBio circular consensus (CCS) and nanopore sequencing, are advantageous in detecting DNA 5-methylcytosine CpGs (5mCpGs), especially repetitive genomic regions. However, existing methods for 5mCpGs using CCS less accurate robust. Here, we present ccsmeth, a deep-learning method to detect reads. We sequence polymerase-chain-reaction treated M.SssI-methyltransferase of one human sample training ccsmeth. Using long (≥10 Kb) reads, ccsmeth...
Abstract The high sequencing error rate has impeded the application of long noisy reads for diploid genome assembly. Most existing assemblers failed to generate high-quality phased assemblies using reads. Here, we present PECAT, a P hased E rror C orrection and A ssembly T ool, reconstructing genomes from We design haplotype-aware correction method that can retain heterozygote alleles while correcting errors. combine corrected read SNP caller raw further improve identification inconsistent...
MicroRNAs (miRNAs) are a class of non-coding RNAs about <inline-formula><tex-math notation="LaTeX">$\sim$</tex-math></inline-formula> 22nt nucleotides. Studies have proven that miRNAs play key roles in many human complex diseases. Therefore, discovering miRNA-disease associations is beneficial to understanding disease mechanisms, developing drugs, and treating It well known it time-consuming expensive process discover the via biological experiments. Alternatively, computational models could...
Drug repositioning is an efficient and promising strategy to identify new indications for existing drugs, which can improve the productivity of traditional drug discovery development. Rapid advances in high-throughput technologies have generated various types biomedical data over past decades, lay foundations furthering development computational approaches. Although many researches tried accuracy by integrating information from multiple sources different levels, it still appealing further...
Abstract Recent advancements in genome assembly have greatly improved the prospects for comprehensive annotation of Transposable Elements (TEs). However, existing methods TE using assemblies suffer from limited accuracy and robustness, requiring extensive manual editing. In addition, currently available gold-standard databases are not comprehensive, even extensively studied species, highlighting critical need an automated detection method to supplement repositories. this study, we introduce...
Identification of essential proteins based on protein interaction network (PIN) is a very important and hot topic in the post genome era. Up to now, number network-based discovery methods have been proposed. Generally, static was constructed by using protein-protein interactions obtained from different experiments or databases. Unfortunately, most are sensitive reliability PIN. In this paper, we propose new method for constructing refined PIN gene expression profiles subcellular location...
The three subsets of virions that comprise the Brome mosaic virus (BMV) were previously thought to be indistinguishable. This work tested hypothesis distinct capsid-RNA interactions in BMV allow different rates viral RNA release. Several results support between capsid and genomic RNAs. First, deletion first eight residues coat protein (CP) resulted RNA1-containing particles having altered morphologies, while those containing RNA2 unaffected. Second, separated by density gradients into a pool...
<title>Abstract</title> <bold>Background</bold>: Dioecy presents significant challenges in plant breeding and evolutionary biology. In <italic>Dioscorea alata</italic> L., the most widely cultivated yam species, dioecy (XY system) a male-biased sex ratio hinder efforts by restricting parental combinations limiting genetic progress. To address these challenges, we present high-quality, phased, telomere-to-telomere genome assembly of male cultivar ‘Kabusa’, comprising 40 chromosomes totaling...
Quantifying the associations between diseases is now playing an important role in modern biology and medicine. Actually discovering could help us gain deeper insights into pathogenic mechanisms of complex diseases, thus lead to improvements disease diagnosis, drug repositioning, development. Due growing body high-throughput biological data, a number methods have been developed for computing similarity during past decade. However, these rarely consider interconnections genes related each...
SUMMARY The Brome mosaic virus (BMV) coat protein (CP) accompanies the three BMV genomic RNAs and subgenomic RNA into out of cells in an infection cycle. In addition to serving as a protective shell for all RNAs, CP plays regulatory roles during process that are mediated through specific binding elements genome. One element is B box present 5′ untranslated region (UTR) RNA1 RNA2 play important formation replication factory, well regulation translation. A second within tRNA‐like 3′ UTR...
Highly portable Oxford Nanopore sequencer producing long reads in real-time at low cost has made many breakthroughs genomics studies. However, a major limitation of nanopore sequencing is its high errors when deciphering DNA sequences from noisy and complex raw data. In this paper, we developed an end-to-end basecaller, SACall, based on convolution layers, transformer self-attention layers CTC decoder. the are used to downsample signals capture local patterns. To achieve contextual relevance...
Abstract Adverse Drug Reactions (ADRs) have a direct impact on human health. As continuous pharmacovigilance and drug monitoring prove to be costly time-consuming, computational methods emerged as promising alternatives. However, most existing primarily focus predicting whether or not the is associated with an adverse reaction do consider core issue of benefit-risk assessment—whether treatment outcome serious when reactions occur. To this end, we categorize clinical outcomes caused by drugs...
Abstract Motivation Nanopore direct RNA sequencing (DRS) enables the detection of N6-methyladenosine (m6A) without extra laboratory techniques. A number supervised or comparative approaches have been developed to identify m6A from DRS reads. However, existing methods typically utilize either statistical features current signals basecalling-error features, ignoring richer information raw Results Here, we propose RedNano, a deep-learning method designed detect reads by utilizing both and...
ABSTRACT The four brome mosaic virus (BMV) RNAs (RNA1 to RNA4) are encapsidated in three distinct virions that have different disassembly rates infection. mechanism for the differential release of BMV from is unknown, since 180 copies same coat protein (CP) encapsidate each genomic RNAs. Using mass spectrometry, we found CP contains a complex pattern posttranslational modifications. Treatment with phosphatase was not significantly affect stability containing RNA1 but impacted RNA2 and...
Abstract Long single-molecular sequencing, such as PacBio circular consensus sequencing (CCS) and nanopore is advantageous in detecting DNA 5-methylcytosine (5mC) CpGs, especially repetitive genomic regions. However, existing methods for 5mCpGs using CCS are less accurate robust. Here, we present ccsmeth, a deep-learning method to detect reads. We sequence PCR-treated M.SssI-treated of one human sample training ccsmeth. Using long (≥10Kb) reads, ccsmeth achieves 0.90 accuracy 0.97 AUC on...
Oxford Nanopore sequencing producing long reads at low cost has made many breakthroughs in genomics studies. However, the large number of errors genome assembly affect accuracy analysis. Polishing is a procedure to correct and can improve reliability downstream performances existing polishing methods are still not satisfactory.We developed novel method, NeuralPolish, assemblies based on alignment matrix construction orthogonal Bi-GRU networks. In this we designed an feature for representing...
Brome mosaic virus (BMV) packages its genomic RNAs (RNA1, RNA2, and RNA3) subgenomic RNA4 into three different particles. However, since the in virions have distinct lengths electrostatic charges, we hypothesize that subsets of should properties. A glutamine to cysteine substitution at position 120 capsid protein (CP) was found result a mutant named QC exhibited dramatically altered ratio virions. RNA2 far more abundant than other RNAs, although ratios could be affected by host plant...