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Identification and analysis of mouse non-coding RNA using transcriptome data

Science China(Life Sciences) 2016年第9期59卷 589-603页

作者： Yuhui Zhao Wanfei Liu jingyao zeng Shoucheng Liu Xinyu Tan Hasanawad Aljohi Songnian Hu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100101 China University of Chinese Academy of Sciences Beijing 100049 China Joint Center for Genomics Research (JCGR) King Abdulaziz City for Science and Technology and Chinese Academy of Sciences Riyadh 11442 Saudi Arabia

Transcripts are expressed spatially and temporally and they are very complicated, precise and specific; however, most studies are focused on protein-coding related genes. Recently, massively parallel c DNA sequencing(RNA-seq) has emerged to be a new and promising tool for transcriptome research, and numbers of non-coding RNAs, especially linc RNAs, have been widely identified and well characterized as important regulators of diverse biological processes. In this study, we used ultra-deep RNA-seq data from 15 mouse tissues to study the diversity and dynamic of non-coding RNAs in mouse. Using our own criteria, we identified totally 16,249 non-coding genes(21,569 non-coding RNAs) in mouse. We annotated these non-coding RNAs by diverse properties and found non-coding RNAs are generally shorter, have fewer exons, express in lower level and are more strikingly tissue-specific compared with protein-coding genes. Moreover, these non-coding RNAs show significant enrichment with transcriptional initiation and elongation signals including histone modifications(H3K4me3, H3K27me3 and H3K36me3), RNAPII binding sites and CAGE tags. The gene set enrichment analysis(GSEA) result revealed several sets of linc RNAs associated with diverse biological processes such as immune effector process, muscle development and sexual reproduction. Taken together, this study provides a more comprehensive annotation of mouse non-coding RNAs and gives an opportunity for future functional and evolutionary study of mouse non-coding RNAs.

关键词：非编码RNA 转录表达小鼠蛋白编码基因组织特异性识别组数生物过程

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高价阳离子(Al^(3+))诱导的Na_(4)Fe_(3)(PO_(4))_(2)(P_(2)O_(7))正极助力构筑全气候钠离子全电池

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Science Bulletin 2024年第6期69卷 772-783页

作者：高金强曾晶垚简伟顺梅雨倪炼山王浩吉王凯胡新宇邓文韬邹国强侯红帅纪效波 College of Chemistry and Chemical Engineering Central South UniversityChangsha 410083China

Na_(4)Fe_(3)(PO_(4))_(2)(P_(2)O_(7))(NFPP)is currently drawing increased attention as a sodium-ion batteries(SIBs)cathode due to the cost-effective and NASICON-type structure features.Owing to the sluggish electron and Na~+conductivities,however,its real implementation is impeded by the grievous capacity decay and inferior rate capability.Herein,multivalent cation substituted microporous Na_(3.9)Fe_(2.9)Al_(0.1)(PO_(4))_(2)(P_(2)O_(7))(NFAPP)with wide operation-temperature is elaborately designed through regulating structure/interface coupled electron/ion transport.Greatly,the derived Na vacancy and charge rearrangement induced by trivalent Al^(3+)substitution lower the ions diffusion barriers,thereby endowing faster electron transport and Na^(+)mobility.More importantly,the existing Al-O-P bonds strengthen the local environment and alleviate the volume vibration during(de)sodiation,enabling highly reversible valence variation and structural evolution.As a result,remarkable cyclability(over 10,000 loops),ultrafast rate capability(200 C),and exceptional all-climate stability(-40-60℃)in half/full cells are demonstrated.Given this,the rational work might provide an actionable strategy to promote the electrochemical property of NFPP,thus unveiling the great application prospect of sodium iron mixed phosphate materials.

关键词： Multivalent cation substitution All-climate Na^(+)mobility Ultrafast rate capability

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Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome

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Genomics, Proteomics & Bioinformatics 2019年第3期17卷 229-247页

作者： Zhenglin Du Liang Ma Hongzhu Qu Wei Chen Bing Zhang Xi Lu Weibo Zhai Xin Sheng Yongqiao Sun Wenjie Li Meng Lei Qiuhui Qi Na Yuan Shuo Shi jingyao zeng Jinyue Wang Yadong Yang Qi Liu Yaqiang Hong Lili Dong Zhewen Zhang Dong Zou Yanqing Wang Shuhui Song Fan Liu Xiangdong Fang Hua Chen Xin Liu Jingfa Xiao Changqing zeng Beijing Institute of Genomics Chinese Academy of SciencesBeijing 100101China BIG Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

To unravel the genetic mechanisms of disease and physiological traits,it requires comprehensive sequencing analysis of large sample size in Chinese populations.Here,we report the primary results of the Chinese Academy of Sciences Precision Medicine Initiative(CASPMI)project launched by the Chinese Academy of Sciences,including the de novo assembly of a northern Han reference genome(NH1.0)and whole genome analyses of 597 healthy people coming from most areas in China.Given the two existing reference genomes for Han Chinese(YH and HX1)were both from the south,we constructed NH1.0,a new reference genome from a northern individual,by combining the sequencing strategies of PacBio,10×Genomics,and Bionano mapping.Using this integrated approach,we obtained an N50 scaffold size of 46.63 Mb for the NH1.0 genome and performed a comparative genome analysis of NH1.0 with YH and HX1.In order to generate a genomic variation map of Chinese populations,we performed the whole-genome sequencing of 597 participants and identified 24.85 million(M)single nucleotide variants(SNVs),3.85 M small indels,and 106,382 structural variations.In the association analysis with collected phenotypes,we found that the T allele of rs1549293 in KAT8 significantly correlated with the waist circumference in northern Han males.Moreover,significant genetic diversity in MTHFR,TCN2,FADS1,and FADS2,which associate with circulating folate,vitamin B12,or lipid metabolism,was observed between northerners and southerners.Especially,for the homocysteine-increasing allele of rs1801133(MTHFR 677T),we hypothesize that there exists a “comfort”zone for a high frequency of 677T between latitudes of 35–45 degree North.Taken together,our results provide a high-quality northern Han reference genome and novel population-specific data sets of genetic variants for use in the personalized and precision medicine.

关键词： De novo assembly Reference genome Variation map Phenotype association Large population

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The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR

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Genomics, Proteomics & Bioinformatics 2020年第6期18卷 749-759页

作者： Shuhui Song Lina Ma Dong Zou Dongmei Tian Cuiping Li Junwei Zhu Meili Chen Anke Wang Yingke Ma Mengwei Li Xufei Teng Ying Cui Guangya Duan Mochen Zhang Tong Jin Chengmin Shi Zhenglin Du Yadong Zhang Chuandong Liu Rujiao Li jingyao zeng Lili Hao Shuai Jiang Hua Chen Dali Han Jingfa Xiao Zhang Zhang Wenming Zhao Yongbiao Xue Yiming Bao China National Center for Bioinformation Beijing 100101China National Genomics Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

On January 22,2020,China National Center for Bioinformation(CNCB)released the 2019 Novel Coronavirus Resource(2019nCoVR),an open-access information resource for the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates,which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline.Of particular note,2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale.It provides all identified variants and their detailed statistics for each virus isolate,and congregates the quality score,functional annotation,and population frequency for each variant.Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available.Moreover,2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019(COVID-19),including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC.Furthermore,by linking with relevant databases in CNCB,2019nCoVR offers data submission services for raw sequence reads and assembled genomes,and data sharing with NCBI.Collectively,SARS-CoV-2 is updated daily to collect the latest information on genome sequences,variants,haplotypes,and literature for a timely reflection,making 2019nCoVR a valuable resource for the global research community.2019nCoVR is accessible at https://***/ncov/.

关键词： 2019nCoVR SARS-CoV-2 Database Genomic variation Haplotype

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The integrative analysis and database construction based on cancer multi-omics data

The integrative analysis and database construction based on ...

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第三届全国系统生物学大会

作者： zeng jingyao Zhang Yadong Shang Yunfei Mai Jialin Xiao Jingfa

Whole-transcriptome mRNA sequencing at single cell resolution(scRNA-seq) is being widely applied to answer many essential questions in developmental biology,immunology,oncology,etc.Particularly with the proliferating studies of human cancers by scRNA-seq technique,massive cancer scRNA-seq datasets were exponentially exploded in the past decade which are calling for a burning demand to be integrated and processed for essential investigations in tumor microenvironment and further comprehensive comparative analysis.To achieve this goal,we developed a database of Cancer Single-cell Expression Map(CancerSCEM,https://***/cancerscem),which consists of 208 cancer samples across 20 human cancer types.A series of uniform and multiscale analyses for each sample were performed,including cell type annotation,expression of functional genes(oncogenes,tumor suppressor genes and widely-used immune checkpoint molecules),cell interaction network,survival analysis and etc.Plus,CancerSCEM was visualized as a user-friendly web interface for users to browse,search,analyze and download all metadata as well as analytical results.More importantly,the newly-constructed comprehensive online analyzing platform in CancerSCEM integrates two analyze modules and seven functions,where investigators can interactively perform cancer scRNA-seq analyses.For example,users can acquire the gene's global expression pattern in a specific sample and rapidly find out cell types that contribute the highest expressions by Gene analyzing module.While in Sample analyzing module,an interaction network for each sample will be visualized indicating cell subsets as key mediators of cellular cross-talk in the specific tumor microenvironment,guiding users to further investigate their underlying biological roles.Taken together,CancerSCEM paved an informative and practical way to facilitate human cancer studies,and also provides insights into clinical therapy assessments.

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基于主客观赋权法的综合能源系统效益评估方法

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广东电力 2023年第1期36卷 1-8页

作者：胡竞秋张轩严心然侯庆峰曾婧瑶邹庄磊中国南方电网有限责任公司北京分公司北京100000 华南理工大学电力学院广东广州510641

为进一步优化综合能源系统的评估与投资,提出一种基于主客观赋权法的综合能源系统经济综合效益评估方法。首先分析多能互补综合能源系统的经济收益特征与构成,确立评价指标选取原则,从经济、能效与低碳性、社会与技术性3个维度建立多层... 详细信息

为进一步优化综合能源系统的评估与投资,提出一种基于主客观赋权法的综合能源系统经济综合效益评估方法。首先分析多能互补综合能源系统的经济收益特征与构成,确立评价指标选取原则,从经济、能效与低碳性、社会与技术性3个维度建立多层级评价指标;进一步,根据指标构成与评价需求,采用层次分析法-反熵权法这种主客观赋权法确定各层级指标权重,并基于归类量化和模糊算法进行指标的归一化处理;最后实现综合经济效益量化评估。算例结果表明,所提出的评价方法可实现客观地分析多能互补综合能源系统经济性、环境与低碳性、社会与技术性3个方面,使用18个4级指标的权重,可以直观、有效、全面多层次地评估多能互补综合能源系统的优劣性,可为综合能源系统建设与运行提供理论指导与决策支撑。

关键词：多能互补综合能源系统综合效益量化层次分析法主客观结合

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高通量计算在大规模人群队列基因组数据解析应用中的挑战

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数据与计算发展前沿 2020年第1期2卷 117-127页

作者：曾瀞瑶苑娜魏文娟李根杜政霖中国科学院北京基因组研究所国家基因组科学数据中心北京100101 人和未来生物科技(长沙)有限公司湖南长沙410152

【目的】为推动精准医学研究的发展,世界各国相继开展大规模人群队列基因组测序计划,通过对数以万计个体进行全基因组测序,构建人群特异的基因组变异图谱。这些海量基因组数据产出,对计算速度和计算通量提出了新的要求,迫切需要速度更... 详细信息

【目的】为推动精准医学研究的发展,世界各国相继开展大规模人群队列基因组测序计划,通过对数以万计个体进行全基因组测序,构建人群特异的基因组变异图谱。这些海量基因组数据产出,对计算速度和计算通量提出了新的要求,迫切需要速度更快、通量更高的计算平台来处理与解读这些生物序列信息。由于基因组数据自身的特点、数据解析过程的多样性和复杂性,致使在大规模人群基因组变异解析中高通量计算资源的使用效率低、计算速度慢、耗时长,服务器与本地数据交换不便,因此需要针对基因组变异解析进行多方面优化,通过软硬件开发来解决应用中存在的多种问题。本文拟对这些优化方法进行分析和综述。【方法】在高通量计算系统中,系统IO瓶颈问题是基因组变异解析并行化效率低的主要原因,通常采用基于分布式非结构化存储数据库以及对象存储系统,以提升IO的大规模可扩展能力,解决分析流程中存在的IO问题;同时通过基因组数据的高效压缩算法,可减少数据IO和传输压力。为了加快基因组数据解析速度,可在软件上采用神经网络等算法优化基因组解析方法,在硬件上使用FPGA(现场可编程逻辑门阵列)或GPU异构计算,以提高数据处理速度。【结果】综合来看,以上多方面的优化可以大幅提升基因组数据分析中高通量计算的性能,解决基因组数据处理中的存储墙问题,提高高通量计算资源的使用效率,大大减少全基因组变异解析的计算时间。【结论】高通量计算在基因组数据解析应用中存在的多种问题,可通过软硬件开发和优化得以解决,从而显著改进高通量计算在大规模人群队列变异解析应用中的计算效率,促进今后人群队列基因组研究与应用的广泛开展。

关键词：高通量计算 IO性能基因组变异解析异构加速数据压缩

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JARID2 coordinates with the NuRD complex to facilitate breast tumorigenesis through response to adipocyte-derived leptin

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Cancer Communications 2023年第10期43卷 1117-1142页

作者： Wei Liu Yi zeng Xinhui Hao Xin Wang Jiaxiang Liu Tianyang Gao Mengdi Wang jingyao Zhang Miaomiao Huo Ting Hu Tianyu Ma Die Zhang Xu Teng Hefen Yu Min Zhang Baowen Yuan Wei Huang Yunkai Yang Yan Wang Key Laboratory of Immune Microenvironment and Disease (Ministry of Education) Department of Biochemistry and Molecular BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinP.R.China Key Laboratory of Cancer and Microbiome State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP.R.China Department of Biochemistry and Molecular Biology School of Basic Medical ScienceSouthwest Medical UniversityLuzhouSichuanP.R.China Department of Breast Surgical Oncology National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP.R.China Beijing Key Laboratory of Cancer Invasion and Metastasis Research Department of Biochemistry and Molecular BiologySchool of Basic Medical SciencesCapital Medical UniversityBeijingP.R.China

Background Proteins containing the Jumonji C(JmjC)domain participated in tumorigenesis and cancer progression.However,the mechanisms underlying this effect are still poorly understood.Our objective was to investigate the role of Jumonji and the AT-rich interaction domain-containing 2(JARID2)—a JmjC family protein—in breast cancer,as well as its latent association with obesity.Methods Immunohistochemistry,The Cancer Genome Atlas,Gene Expression Omnibus,and other databases were used to analyze the expression of JARID2 in breast cancer cells.Growth curve,5-ethynyl-2-deoxyuridine(EdU),colony formation,and cell invasion experiments were used to detect whether JARID2 affected breast cancer cell proliferation and invasion.Spheroidization-based experiments and xenotumor transplantation in NOD/SCID mice were used to examine the association between JARID2 and breast cancer stemness.RNA-sequencing,Kyoto Encyclopedia of Genes and Genomes,and Gene Set Enrichment Analysis were used to identify the cell processes in which JARID2 participates.Immunoaffinity purification and silver staining mass spectrometry were conducted to search for proteins that might interact with JARID2.The results were further verified using co-immunoprecipitation and glutathione S-transferase(GST)pull-down experiments.Using chromatin immunoprecipitation(ChIP)sequencing,we sought the target genes that JARID2 and metastasis-associated protein 1(MTA1)jointly regulated;the results were validated by ChIP-PCR,quantitative ChIP(qChIP)and ChIP-reChIP assays.A coculture experiment was used to explore the interactions between breast cancer cells and adipocytes.Results In this study,we found that JARID2 was highly expressed in multiple types of cancer including breast cancer.JARID2 promoted glycolysis,lipid metabolism,proliferation,invasion,and stemness of breast cancer cells.Furthermore,JARID2 physically interacted with the nucleosome remodeling and deacetylase(NuRD)complex,transcriptionally repressing a series of tumor suppressor genes such as BRCA2 DNA repair as

关键词： breast tumorigenesis JARID2 metabolism the NuRD complex tumor suppressor genes

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Q690钢-高强螺栓承压型抗剪连接试验

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重庆大学学报 2022年第7期45卷 24-36页

作者：李静尧聂诗东曾佳戴国欣重庆大学土木工程学院重庆400045 重庆大学山地城镇建设与新技术教育部重点试验室重庆400045 中国建筑西南设计研究院有限公司成都610093

对32组Q690高强钢高强螺栓(10.9级或12.9级)抗剪连接进行试验,观察到连接钢板的剪出破坏、撕裂破坏、承压破坏、净截面破坏和螺栓剪切破坏共5种破坏模式。通过分析试验数据,发现Q690高强钢有良好的局部变形能力,研究了螺栓等级、规格、... 详细信息

对32组Q690高强钢高强螺栓(10.9级或12.9级)抗剪连接进行试验,观察到连接钢板的剪出破坏、撕裂破坏、承压破坏、净截面破坏和螺栓剪切破坏共5种破坏模式。通过分析试验数据,发现Q690高强钢有良好的局部变形能力,研究了螺栓等级、规格、预拉力和端距、边距对试件承载力和变形的影响。收集了多篇文献中的试验数据,得到剪出破坏、撕裂破坏的几何界限约为(0.7~0.9)e_(1)/e_(2),净截面破坏试件的应力比均大于1.0。

关键词： Q690钢高强钢高强螺栓承压型连接抗剪连接

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切换通信拓扑下多智能体系统自适应跟踪控制

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厦门大学学报（自然科学版） 2023年第4期62卷 598-604页

作者：王靖瑶李依格曾建平厦门大学航空航天学院福建厦门361102

针对多智能体系统的跟踪控制问题,提出一种基于随机切换通信拓扑的多智能体系统自适应跟踪控制方法.假设智能体间的通信拓扑是随机切换的,并且切换过程由连续时间马尔科夫随机过程描述.本文给出了一种完全分布式的跟踪控制协议,该协议... 详细信息

针对多智能体系统的跟踪控制问题,提出一种基于随机切换通信拓扑的多智能体系统自适应跟踪控制方法.假设智能体间的通信拓扑是随机切换的,并且切换过程由连续时间马尔科夫随机过程描述.本文给出了一种完全分布式的跟踪控制协议,该协议仅需要每个节点的局部信息来更新控制输入,使得跟随者仅使用局部信息即可在均方意义下跟踪领导者的状态,而无需使用任何全局信息.最后,通过实现编队控制任务证明了给出控制方法的有效性.

关键词：多智能体系统马尔科夫随机切换拓扑完全分布式一致性算法编队控制

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