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Chromosome-scale assembly of the Kandelia obovata genome

Horticulture Research 2020年第1期7卷 1823-1834页

作者： Min-Jie Hu Wei-Hong Sun Wen-Chieh Tsai shuang Xiang Xing-Kai Lai De-Qiang Chen Xue-Die Liu Yi-Fan Wang Yi-Xun Le Si-Ming Chen Di-Yang Zhang Xia Yu Wen-Qi Hu Zhuang Zhou Yan-Qiong Chen shuang-quan zou Zhong-Jian Liu Key Laboratory of Humid Sub-tropical Eco-Geographical Processes of the Ministry of Education Fujian Normal UniversityFuzhou 350007China Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources College of ForestryFujian Agriculture and Forestry UniversityFuzhou 350002China Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture Fujian Agriculture and Forestry UniversityFuzhou 350002China Institute of Tropical Plant Sciences and Microbiology National Cheng Kung UniversityTainan 701China Administration of the quanzhou Bay Estuary Wetland Nature Reserve Quanzhou 362000China Ocean College Minjiang UniversityFuzhou 350002China Henry Fok College of Biology and Agriculture Shaoguan UniversityShaoguan 512005China

The mangrove Kandelia obovata(Rhizophoraceae)is an important coastal shelterbelt and landscape tree distributed in tropical and subtropical areas across East Asia and Southeast ***,a chromosome-level reference genome of *** based on PacBio,Illumina,and Hi-C data is *** high-quality assembled genome size is 177.99 Mb,with a contig N50 value of 5.74 Mb.A large number of contracted gene families and a small number of expanded gene families,as well as a small number of repeated sequences,may account for the small *** *** found that *** experienced two whole-genome polyploidization events:one whole-genome duplication shared with other Rhizophoreae and one shared with most eudicots(γevent).We confidently annotated 19,138 protein-coding genes in *** and identified the MADS-box gene class and the RPW8 gene class,which might be related to flowering and resistance to powdery mildew in *** and Rhizophora apiculata,*** reference *** genome described here will be very useful for further molecular elucidation of various traits,the breeding of this coastal shelterbelt species,and evolutionary studies with related taxa.

关键词： breeding coastal landscape

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The camphor tree genome enhances the understanding of magnoliid evolution

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Journal of Genetics and Genomics 2022年第3期49卷 249-253页

作者： Wei-Hong Sun shuang Xiang Qi-Gong Zhang Lin Xiao Diyang Zhang Peilan Zhang De-Qiang Chen Yang Hao, Ding-Kun Liu Le Ding Yifan Li Hui Ni Yifan Wang Xi Wu Fu-Hui Liu Guo-Rui Chen Guo-Yong Han Jin-Zhang Chen Bao-Chun Su Jin-Xing Gao Xiao-Hui Wan Zhiwen Wang Yicun Chen Yang-Dong Wang Wei Huang Bobin Liu Xiao-Xing zou Lin Ni Zhong-Jian Liu shuang-quan zou College of Forestry Fujian Agriculture and ForestryFuzhouFujian 350002China Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources Fujian Agriculture and ForestryFuzhouFujian 350002China Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China Fuzhou Botanical Garden FuzhouFujian 350002China quanzhou Forestry Bureau QuanzhouFujian 362000China Pub Bio-Tech WuhanHubei 430070China Research Institute of Subtropical Forestry Chinese Academy of ForestryHangzhouZhejiang 311400China

Magnoliids represent the third largest branch of the most diverse and species-rich angiosperms,and their phylogenetic position relative to monocots and eudicots remains uncertain(Dong et al.,2021).Here,we describe the assembly of a high-quality chromosome-level genome sequence for Cinnamomum camphora(camphor),an evergreen tree belonging to *** phylogenetic analysis indicated possible incomplete lineage sorting(ILS)during the rapid diversification of the early diverging branches of angiosperms,which may have led to the unstable phylogenetic position of magnoliids.

关键词： sorting tree incomplete

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The Phoebe genome sheds light on the evolution of magnoliids

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Horticulture Research 2020年第1期7卷 876-888页

作者： Shi-Pin Chen Wei-Hong Sun Yuan-Fang Xiong Yu-Ting Jiang Xue-Die Liu Xing-Yu Liao Di-Yang Zhang Shu-Zhen Jiang Yu Li Bin Liu Liang Ma Xia Yu Li He Bao Liu Jin-Lin Feng Li-Zhen Feng Zhi-Wen Wang shuang-quan zou Si-Ren Lan Zhong-Jian Liu College of Forestry Fujian Agriculture and Forestry University350002 FuzhouChina Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture Fujian Agriculture and Forestry University350002 FuzhouChina PubBio-Tech 430070 WuhanChina Zhejiang Institute of Subtropical Crops Zhejiang Academy of Agricultural Sciences325005 WenzhouChina Institute of Vegetable and Flowers Shandong Academy of Agricultural Sciences250100 JinanChina

Lauraceae includes the genus Phoebe,and the family is linked to the evolution of *** sequenced the genome of Phoebe bournei *** assembled genome size was 989.19 Mb,with a contig N50 value of 2.05 Mb.A total of 28,198 protein-coding genes were annotated in ***-genome duplication(WGD)analysis showed that Lauraceae has experienced two WGD events;the older WGD event occurred just before the divergence of Lauraceae and Magnoliales,and the more recent WGD was shared by all lineages of *** phylogenetic tree showed that magnoliids form a sister clade to monocots and *** also identified 63 MADS-box genes,including AGL12-like genes that may be related to the regulation of *** roots and FIN219-like genes encoding GH3 proteins,which are involved in ***50-like genes involved in light signal-mediated pedicel or stem development were also *** ATMYB46-and three PtrEPSP-homologous genes related to lignin biosynthesis were *** genes may be associated with the formation of straight trunks in ***,the *** reference genome provides insight into the origin,evolution,and diversification of Phoebe and other magnoliids.

关键词： Whole evolution light

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A Machine Learning Method for Differentiating and Predicting Human-Infective Coronavirus Based on Physicochemical Features and Composition of the Spike Protein

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Chinese Journal of Electronics 2021年第5期30卷 815-823页

作者： WANG Chao zou quan Institute of Fundamental and Frontier Sciences University of Electronic Science and Technology of China Hainan Key Laboratory for Computational Science and Application Hainan Normal University

Several Coronaviruses(CoVs) are epidemic pathogens that cause severe respiratory syndrome and are associated with significant morbidity and mortality. In this paper, a machine learning method was developed for predicting the risk of human infection posed by CoVs as an early warning system. The proposed Spike-SVM(Support vector machine) model achieved an accuracy of 97.36% for Human-infective CoV(HCoV) and Nonhuman-infective CoV(Non-HCoV) classification. The top informative features that discriminate HCoVs and Non-HCoVs were identified. Spike-SVM is anticipated to be a useful bioinformatics tool for predicting the infection risk posed by CoVs to humans.

关键词： Spike protein NonHCoVs genetics microorganisms Support vector machine mortality Spike-SVM model Human-infective CoV severe respiratory syndrome machine learning method biology computing predicting Human-infective coronavirus diseases proteins HCoV human infection differentiating Nonhuman-infective CoV infection risk CoVs discriminate HCoVs learning (artificial intelligence) bioinformatics support vector machines informative features significant morbidity molecular biophysics early warning system epidemic pathogens Coronaviruses

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Trends and Potential of Machine Learning and Deep Learning in Drug Study at Single-Cell Level

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Research 2023年第4期2023卷 145-162页

作者： Ren Qi quan zou Yangtze Delta Region Institute(Quzhou) University of Electronic Science and Technology of ChinaQuzhou 324000China School of Life Science and Technology University of Electronic Science and Technology of ChinaChengduChina Institute of Fundamental and Frontier Sciences University of Electronic Science and Technology of ChinaChengduChina.

Cancer treatments always face challenging problems,particularly drug resistance due to tumor cell *** existing datasets include the relationship between gene expression and drug sensitivities;however,the majority are based on tissue-level *** drugs at the single-cell level are perspective to overcome minimal residual disease caused by subclonal resistant cancer cells retained after initial curative ***,machine learning techniques can help us understand how different types of cells respond to different cancer drugs from the perspective of single-cell gene *** modeling using single-cell data and drug response information will not only improve machine learning for cell-drug outcome prediction but also facilitate the discovery of drugs for specific cancer subgroups and specific cancer *** this paper,we review machine learning and deep learning approaches in drug *** analyzing the application of these methods on cancer cell lines and single-cell data and comparing the technical gap between single-cell sequencing data analysis and single-cell drug sensitivity analysis,we hope to explore the trends and potential of drug research at the single-cell data level and provide more inspiration for drug research at the single-cell *** anticipate that this review will stimulate the innovative use of machine learning methods to address new challenges in precision medicine more broadly.

关键词： drugs expression overcome

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Model-driven full system dynamics estimation of PMSM-driven chain shell magazine

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Defence Technology（防务技术） 2024年第9期39卷 147-156页

作者： Kai Wei Longmiao Chen quan zou School of Mechanical Engineering NanJing University of Science and TechnologyNanjing210094China

Based on the system dynamic model, a full system dynamics estimation method is proposed for a chain shell magazine driven by a permanent magnet synchronous motor(PMSM). An adaptive extended state observer(AESO) is proposed to estimate the unmeasured states and disturbance, in which the model parameters are adjusted in real time. Theoretical analysis shows that the estimation errors of the disturbances and unmeasured states converge exponentially to zero, and the parameter estimation error can be obtained from the extended state. Then, based on the extended state of the AESO, a novel parameter estimation law is designed. Due to the convergence of AESO, the novel parameter estimation law is insensitive to controllers and excitation signal. Under persistent excitation(PE) condition, the estimated parameters will converge to a compact set around the actual parameter value. Without PE signal, the estimated parameters will converge to zero for the extended state. Simulation and experimental results show that the proposed method can accurately estimate the unmeasured states and disturbance of the chain shell magazine, and the estimated parameters will converge to the actual value without strictly continuous PE signals.

关键词： Chain shell magazine Full system dynamics estimation Disturbance estimation Parameter estimation Adaptive extended state observer

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DeepM6ASeq-EL:prediction of human N6-methyladenosine(m^(6)A)sites with LSTM and ensemble learning

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Frontiers of Computer Science 2022年第2期16卷 27-33页

作者： Juntao CHEN quan zou Jing LI Institute of Fundamental and Frontier Sciences University of Electronic Science and Technology of ChinaChengdu 610051China Hainan Key Laboratory for Computational Science and Application Hainan Normal UniversityHaikou 571158China College of Intelligence and Computing Tianjin UniversityTianjin 300350China

N6-methyladenosine(m^(6)A)is a prevalent methylation modification and plays a vital role in various biological processes,such as metabolism,mRNA processing,synthesis,and *** studies have suggested that m^(6)A modification is related to common diseases such as cancer,tumours,and ***,accurate prediction of methylation sites in RNA sequences has emerged as a critical issue in the area of ***,traditional high-throughput sequencing and wet bench experimental techniques have the disadvantages of high costs,significant time requirements and inaccurate identification of *** through the use of traditional experimental methods,researchers have produced many large databases of m^(6)A *** the support of these basic databases and existing deep learning methods,we developed an m^(6)A site predictor named DeepM6ASeq-EL,which integrates an ensemble of five LSTM and CNN classifiers with the combined strategy of hard *** to the state-of-the-art prediction method WHISTLE(average AUC 0.948 and 0.880),the DeepM6ASeq-EL had a lower accuracy in m^(6)A site prediction(average AUC:0.861 for the full transcript models and 0.809 for the mature messenger RNA models)when tested on six independent datasets.

关键词： N6-methyladenosine site prediction LSTM CNN ensemble learning

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String kernels construction and fusion:a survey with bioinformatics application

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Frontiers of Computer Science 2022年第6期16卷 145-158页

作者： Ren QI Fei GUO quan zou College of Intelligence and Computing Tianjin UniversityTianjin300350China Institute of Fundamental and Frontier Sciences University of Electronic Science and Technology of ChinaChengdu610056China Hainan Key Laboratory for Computational Science and Application Hainan Normal UniversityHaikou571158China

The kernel method,especially the kernel-fusion method,is widely used in social networks,computer vision,bioinformatics,and other *** deals effectively with nonlinear classification problems,which can map linearly inseparable biological sequence data from low to high-dimensional space for more accurate differentiation,enabling the use of kernel methods to predict the structure and function of ***,the kernel method is significant in the solution of bioinformatics *** kernels applied in bioinformatics are explained clearly,which can help readers to select proper kernels to distinguish *** biological sequence data occur in practical *** of the use of machine learning methods to obtain knowledge,and how to explore the structure and function of biological methods for theoretical prediction,have always been emphasized in *** kernel method has gradually become an important learning algorithm that is widely used in gene expression and biological sequence *** review focuses on the requirements of classification tasks of biological sequence *** studies kernel methods and optimization algorithms,including methods of constructing kernel matrices based on the characteristics of biological sequences and kernel fusion methods existing in a multiple kernel learning framework.

关键词： multiple kernel learning kernel fusion methods support vector machines biological sequences analysis

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Is combined lipid-regulating therapy safe and feasible for the very old patients with mixed dyslipidemia?

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Journal of Geriatric Cardiology 2013年第4期10卷 349-354页

作者： Xiao zou quan-Jin Si The First Department of the Geriatric Cardiology Chinese PLA General Hospital NO.28 Fuxing Road Beijing 100853 China

OBJECTIVES: To detect the efficacy and safety of combined lipid-regulating therapies in the very old patients with mixed dyslipidemia and determine an appropriate therapy for them。 METHODS: Four hundred and fifty patients aged over 75 with mixed dyslipidemia were divided into five groups according to different combination therapies。 Lipid levels and drug related adverse events were tested during the study。 RESULTS: Total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) levels were reduced in every group compared to baseline: statin + ezetimibe: -30.0% and -55.5%; statin + policosanol: -31.1% and -51.2%; statin + fibrates: -23.7% and -44.6%; statin + niacin: -25.2% and -43.0%; and niacin + fibrates: -11。3% and -23.5%。 The target achievement rates of LDL-C all exceeded 50%, except in niacin + fibrates (42.0%); statin + ezetimibe: 57.0%; statin + policosanol: 56.0%; statin + niacin: 52.0%; and statin + fibrates: 50.0%。 However, overall, the niacin + fibrates group was the most effective in decreasing triglyceride (TG) and increasing high-density lipoprotein cholesterol (HDL-C) as follows: niacin + fibrates: -39.3% and 28.6%; statin + fibrates: -29.3% and 18.4%; statin + niacin: -18.5% and 16.7%; statin + ezetimibe: -17.1% and 7.1%; and statin + policosanol: -15.6% and 9.5%。 The achievement rates of TG and HDL-C levels in niacin + fibrates (58.0% and 39.0%) were better than the other four groups: statin + niacin (34.0% and 34.0%), statin + fibrates (43.0% and 28.0%), statin + policosanol (30.0% and 24.0%) and statin + ezetimibe (28.0% and 25.0%)。 Patients in all five groups experiencing drug adverse events were only 2% and no severe adverse events occurred。 CONCLUSIONS: Statin + ezetimibe was the most effective group in lowering TC and LDL-C levels, while niacin + fibrates was the most effective in decreasing TG and increasing HDL-C levels。 The commonly used combined lipid-regulating therapies with common dosages in this study were all quite safe and fea

关键词： Combination therapies Elderly patients Mixed dyslipidemia Safety

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Effect of Eliminating Edges on Robustness of Scale-Free Networks under Intentional Attack

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Chinese Physics Letters 2010年第6期27卷 270-272页

作者： LI Yong WU Jun zou An-quan Department of Business Administration Changsha University Changsha 410073 College of Information Systems and Management National University of Defense Technology Changsha 410073

We study the robustness of complex networks under edge elimination. We propose three different edge elimination strategies and investigate their effects on the robustness of scale-free networks under intentional attack. We show that deleting a proper fraction of edges connecting hub nodes and hub nodes can enhance the robustness of scale-free networks under intentional attack.

关键词： Scales Nodes

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