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| 1 | The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types显示文摘The Genome Sequence Archive(GSA)is a data repository for archiving raw sequence data,which provides data storage and sharing services for worldwide scientific communities.Considering explosive data growth with diverse data types,here we present the GSA family by expanding into a set of resources for raw data archive with different purposes,namely,GSA(https://ngdc.cncb.ac.cn/gsa/),GSA for Human(GSA-Human,https://ngdc.cncb.ac.cn/gsa-human/),and Open Archive for Miscellaneous Data(OMIX,https://ngdc.cncb.ac.cn/omix/).Compared with the 2017 version,GSA has been significantly updated in data model,online functionalities,and web interfaces.GSA-Human,as a new partner of GSA,is a data repository specialized in human genetics-related data with controlled access and security.OMIX,as a critical complement to the two resources mentioned above,is an open archive for miscellaneous data.Together,all these resources form a family of resources dedicated to archiving explosive data with diverse types,accepting data submissions from all over the world,and providing free open access to all publicly available data in support of worldwide research activities. | Tingting Chen Xu Chen Sisi Zhang Junwei Zhu Bixia Tang Anke Wang Lili Dong Zhewen Zhang Caixia Yu Yanling Sun Lianjiang Chi Huanxin Chen Shuang Zhai Yubin Sun Li Lan Xin Zhang Jingfa Xiao Yiming Bao Yanqing Wang Zhang Zhang Wenming Zhao | 2021 | Genomics, Proteomics & Bioinformatics2021，19，4： | 38 |
| 2 | MicroRNA expression profiling in diabetic GK rat model显示文摘MicroRNAs (miRNAs ) 是小搁浅单人赛的非编码的 RNA 的一个最新识别的班,经由 post-transcriptional 调整他们的目标基因小径。miRNAs 在许多生物过程起重要作用,这被证明了。为了更好理解 miRNA,在类型 2 糖尿病上工作,我们使用了 oligonucleotide microarray 监视 GotoKakizaki (GK ) 和 Wistar 老鼠的骨胳的肌肉的 miRNA 表达式侧面。七 miRNAs 是下面表示的,二 miRNAs 在 GK 老鼠的肌肉是过去表示的,这被发现。在他们之中, miR-24 显示出最突出的变化。p38 MAPK,是 miR-24 的一个直接目标,也显示出表示差别。所有数据给 miR-24 可能通过 p38 MAPK 的下面规定与糖尿病被联系的线索。 | Bing Huang Wenming Qin Botao Zhao Yi Shi Chengguo Yao Jin Li Huasheng Xiao Youxin Jin | 2009 | Acta Biochimica et Biophysica Sinica2009，41，6： | 17 |
| 3 | GSA:Genome Sequence Archive显示文摘With the rapid development of sequencing technologies towards higher throughput and lower cost, sequence data are generated at an unprecedentedly explosive rate. To provide an efficient and easy-to-use platform for managing huge sequence data, here we present Genome Sequence Archive(GSA; http://bigd.big.ac.cn/gsa or http://gsa.big.ac.cn), a data repository for archiving raw sequence data. In compliance with data standards and structures of the International Nucleotide Sequence Database Collaboration(INSDC), GSA adopts four data objects(Bio Project, Bio Sample,Experiment, and Run) for data organization, accepts raw sequence reads produced by a variety of sequencing platforms, stores both sequence reads and metadata submitted from all over the world,and makes all these data publicly available to worldwide scientific communities. In the era of big data, GSA is not only an important complement to existing INSDC members by alleviating the increasing burdens of handling sequence data deluge, but also takes the significant responsibility for global big data archive and provides free unrestricted access to all publicly available data in support of research activities throughout the world. | Yanqing Wang Fuhai Song Junwei Zhu Sisi Zhang Yadong Yang Tingting Chen Bixia Tang Lili Dong Nan Ding Qian Zhang Zhouxian Bai Xunong Dong Huanxin Chen Mingyuan Sun Shuang Zhai Yubin Sun Lei Yu Li Lan Jingfa Xiao Xiangdong Fang Hongxing Lei Zhang Zhang Wenming Zhao | 2017 | Genomics, Proteomics & Bioinformatics2017，15，1： | 13 |
| 4 | Genome Warehouse: A Public Repository Housing Genome-scale Data显示文摘The Genome Warehouse(GWH)is a public repository housing genome assembly data for a wide range of species and delivering a series of web services for genome data submission,storage,release,and sharing.As one of the core resources in the National Genomics Data Center(NGDC),part of the China National Center for Bioinformation(CNCB;https://ngdc.cncb.ac.cn),GWH accepts both full and partial(chloroplast,mitochondrion,and plasmid)genome sequences with different assembly levels,as well as an update of existing genome assemblies.For each assembly,GWH collects detailed genome-related metadata of biological project,biological sample,and genome assembly,in addition to genome sequence and annotation.To archive high-quality genome sequences and annotations,GWH is equipped with a uniform and standardized procedure for quality control.Besides basic browse and search functionalities,all released genome sequences and annotations can be visualized with JBrowse.By May 21,2021,GWH has received 19,124 direct submissions covering a diversity of 1108 species and has released 8772 of them.Collectively,GWH serves as an important resource for genomescale data management and provides free and publicly accessible data to support research activities throughout the world.GWH is publicly accessible at https://ngdc.cncb.ac.cn/gwh. | Meili Chen Yingke Ma Song Wu Xinchang Zheng Hongen Kang Jian Sang Xingjian Xu Lili Hao Zhaohua Li Zheng Gong Jingfa Xiao Zhang Zhang Wenming Zhao Yiming Bao | 2021 | Genomics, Proteomics & Bioinformatics2021，19，4： | 12 |
| 5 | Status quo and development trend of lost foam casting technology显示文摘Lost foam casting(LFC)technology has been widely applied to cast iron and cast steel.However,the development of LFC for Al and Mg alloys was relatively slower than that for cast iron and cast steel.The application of LFC to Al and Mg alloys needs more effort,especially in China.In this paper,the development history of LFC is reviewed,and the application situations of LFC to Al and Mg alloys are mainly discussed.Meanwhile,the key problems of LFC for Al and Mg alloys are also pointed out.Finally,the prospects for LFC technology are discussed,and some special new LFC technologies are introduced for casting Al and Mg alloys.In future,the development trends of green LFC technology mainly focus on the special new LFC methods,metal material,coating,heat treatment,new foam materials as well as purification technology of tail gas,etc. | Fan Zitian Jiang Wenming Liu Fuchu Xiao Botao | 2014 | China Foundry2014，11，4： | 6 |
| 6 | A Fiber Tractography Study of Social-Emotional Related Fiber Tracts in Children and Adolescents with Autism Spectrum Disorder显示文摘The symptoms of autism spectrum disorder(ASD) have been hypothesized to be caused by changes in brain connectivity. From the clinical perspective, the‘‘disconnectivity'' hypothesis has been used to explain characteristic impairments in ‘‘socio-emotional'' function.Therefore, in this study we compared the facial emotional recognition(FER) feature and the integrity of socialemotional-related white-matter tracts between children and adolescents with high-functioning ASD(HFA) and their typically developing(TD) counterparts. The correlation between the two factors was explored to find out if impairment of the white-matter tracts is the neural basis of social-emotional disorders. Compared with the TD group,FER was significantly impaired and the fractional anisotropy value of the right cingulate fasciculus was increased in the HFA group(P \ 0.01). In conclusion, the FER function of children and adolescents with HFA was impaired and the microstructure of the cingulate fasciculus had abnormalities. | Yun Li Hui Fang Wenming Zheng Lu Qian Yunhua Xiao Qiaorong Wu Chen Chang Chaoyong Xiao Kangkang Chu Xiaoyan Ke | 2017 | Neuroscience Bulletin2017，33，6： | 5 |
| 7 | The Tibetan Plateau Surface–Atmosphere Coupling System and Its Weather and Climate Effects: The Third Tibetan Plateau Atmospheric Science Experiment显示文摘The Tibetan Plateau(TP) is a key area affecting forecasts of weather and climate in China and occurrences of extreme weather and climate events over the world. The China Meteorological Administration, the National Natural Science Foundation of China, and the Chinese Academy of Sciences jointly initiated the Third Tibetan Plateau Atmospheric Science Experiment(TIPEX-Ⅲ) in 2013, with an 8–10-yr implementation plan. Since its preliminary field measurements conducted in 2013, routine automatic sounding systems have been deployed at Shiquanhe, Gaize, and Shenzha stations in western TP, where no routine sounding observations were available previously. The observational networks for soil temperature and soil moisture in the central and western TP have also been established. Meanwhile, the plateau-scale and regional-scale boundary layer observations, cloud–precipitation microphysical observations with multiple radars and aircraft campaigns, and tropospheric–stratospheric air composition observations at multiple sites, were performed. The results so far show that the turbulent heat exchange coefficient and sensible heat flux are remarkably lower than the earlier estimations at grassland, meadow, and bare soil surfaces of the central and western TP. Climatologically, cumulus clouds over the main body of the TP might develop locally instead of originating from the cumulus clouds that propagate northward from South Asia. The TIPEX-Ⅲ observations up to now also reveal diurnal variations, macro-and microphysical characteristics, and water-phase transition mechanisms, of cumulus clouds at Naqu station. Moreover, TIPEX-Ⅲ related studies have proposed a maintenance mechanism responsible for the Asian 'atmospheric water tower' and demonstrated the effects of the TP heating anomalies on African, Asian, and North American climates. Additionally, numerical modeling studies show that the Γ distribution of raindrop size is more suitable for depicting the TP raindrop characteristics compared to the M–P distribution, the overestimation of sensible heat flux can be reduced via modifying the heat transfer parameterization over the TP, and considering climatic signals in some key areas of the TP can improve the skill for rainfall forecast in the central and eastern parts of China. Furthermore, the TIPEX-Ⅲ has been promoting the technology in processing surface observations, soundings, and radar observations, improving the quality of satellite retrieved soil moisture and atmospheric water vapor content products as well as high-resolution gauge–radar–satellite merged rainfall products, and facilitating the meteorological monitoring, forecasting, and data sharing operations. | Ping ZHAO Yueqing LI Xueliang GUO Xiangde XU Yimin LIU Shihao TANG Wenming XIAO Chunxiang SHI Yaoming MA Xing YU Huizhi LIU La JIA Yun CHEN Yanju LIU Jian LI Dabiao LUO Yunchang CAO Xiangdong ZHENG Junming CHEN An XIAO Fang YUAN Donghui CHEN Yang PANG Zhiqun HU Shengjun ZHANG Lixin DONG Juyang HU Shuai HAN Xiuji ZHOU | 2019 | Journal of Meteorological Research2019，33，3： | 4 |
| 8 | eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses显示文摘It has become increasingly challenging for researchers to analyze the exponentially expanding amount of multi-omic data.Here,we describe multi-functional software named evolutionary GenotypePhenotype Systems(eGPS)that enables users to perform comprehensive multiomic and evolutionary analyses.The eGPS combines the power of cloud computing and the advantage of desktop application,has a user-friendly graphic interface and is highly interactive. | Dalang Yu Lili Dong Fangqi Yan Hailong Mu Bixia Tang Xiao Yang Tao Zeng Qing Zhou Feng Gao Zhonghuang Wang Ziqian Hao Hongen Kang Yi Zheng Hongwei Huang Yuzhang Wei Wei Pan Yaochen Xu Junwei Zhu Shilei Zhao Ciran Wang Pengyu Wang Long Dai Mushan Li Li Lan Yiwei Wang Hua Chen Yi-Xue Li Yun-Xin Fu Zhen Shao Yiming Bao Fangqing Zhao Luo-Nan Chen Guo-Qing Zhang Wenming Zhao Haipeng Li | 2019 | National Science Review2019，6，5： | 4 |
| 9 | The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR显示文摘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://bigd.big.ac.cn/ncov/. | 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 | 2020 | Genomics, Proteomics & Bioinformatics2020，18，6： | 4 |
| 10 | Bin-based model construction and analytical strategies for dissecting complex traits with chromosome segment substitution lines显示文摘Chromosome segment substitution lines have been created in several experimental models,including many plant and animal species,and are useful tools for the genetic analysis and mapping of complex traits.The traditional t-test is usually applied to identify a quantitative trait locus (QTL) that is contained within a chromosome segment to estimate the QTL's effect.However,current methods cannot uncover the entire genetic structure of complex traits.For example,current methods cannot distinguish between main effects and epistatic effects.In this paper,a linear epistatic model was constructed to dissect complex traits.First,all the long substituted segments were divided into overlapping small bins,and each small bin was considered a unique independent variable.The genetic model for complex traits was then constructed.When considering all the possible main effects and epistatic effects,the dimensions of the linear model can become extremely high.Therefore,variable selection via stepwise regression (Bin-REG) was proposed for the epistatic QTL analysis in the present study.Furthermore,we tested the feasibility of using the LASSO (least absolute shrinkage and selection operator) algorithm to estimate epistatic effects,examined the fully Bayesian SSVS (stochastic search variable selection) approach,tested the empirical Bayes (E-BAYES) method,and evaluated the penalized likelihood (PENAL) method for mapping epistatic QTLs.Simulation studies suggested that all of the above methods,excluding the LASSO and PENAL approaches,performed satisfactorily.The Bin-REG method appears to outperform all other methods in terms of estimating positions and effects. | TANG ZaiXiang XIAO Jing HU WenMing YU Bo XU ChenWu | 2012 | Chinese Science Bulletin2012，57，21： | 1 |
| 11 | Towards temperature driven forward osmosis desalination using Semi-IPN hydrogels as reversible draw agents显示文摘 | Yufeng Cai Wenming Shen Siew Leng Loo William B. Krantz Rong Wang Anthony G. Fane Xiao Hu | 2013 | Water Research2013，，11： | 1 |
| 12 | Structureand crystallization kinetics of Bi2O3-B2O3 glasses显示文摘 | Yin Cheng Xiao Hanning Guo Wenming | 2006 | Thermochimica Acta2006，444，： | 1 |
| 13 | Effect of A1203 content on BaO-A~03-B203-SiO2 glass sealant for solid oxide fuel cell显示文摘 | Sun Tao Xiao HannhN Guo Wenming | 2010 | Ceramics International2010，36，2： | 1 |
| 14 | Effect of A1203 content on BaO - A1203 - BzO3 - SiOz glass sealant for sol- id oxide fuel eell显示文摘 | Tao Sun Hanning Xiao Wenming Guo Xiucheng Hong | 2010 | 36:821-8262010，36，： | 1 |
| 15 | Influence of rare-earth oxides on structure and crystallization properties of Bi 2 O 3 –B 2 O 3 glass显示文摘 | Yin Cheng Hanning Xiao Wenming Guo | 2007 | Materials Science & Engineering A2007，，1： | 1 |
| 16 | Influence of rare-earth oxides on structnre and crystallization properties of Bi2O3B2O3 glass显示文摘 | Yin Cheng Hanning Xiao Wenming Guo | 2008 | Materials Science and Engineering: A2008，480，12： | 1 |
| 17 | High-density lipoprotein is a potential growth factor for adrenocortical cells显示文摘 | Koji Murao Hitomi Imachi Wenming Cao Xiao Yu Junhua Li Kazuya Yoshida Rania A.M. Ahmed Kensuke Matsumoto Takamasa Nishiuchi Norman C.W. Wong Toshihiko Ishida | 2006 | Biochemical and Biophysical Research Communications2006，，1： | 1 |
| 18 | Effect of Al 2 O 3 content on BaO–Al 2 O 3 –B 2 O 3 –SiO 2 glass sealant for solid oxide fuel cell显示文摘 | Tao Sun Hanning Xiao Wenming Guo Xiucheng Hong | 2009 | Ceramics International2009，，2： | 1 |
| 19 | Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine显示文摘High-throughput next generation sequencing (NGS) is a shotgun approach applied in a parallel fashion by which the genome is fragmented and sequenced through small pieces and then analyzed either by aligning to a known reference genome or by de novo assembly without reference genome.This technology has led researchers to conduct an explosion of sequencing related projects in multidisciplinary fields of science.However,due to the limitations of sequencing-based chemistry,length of sequencing reads and the complexity of genes,it is difficult to determine the sequences of some portions of the human genome,leaving gaps in genomic data that frustrate further analysis.Particularly,some complex genes are difficult to be accurately sequenced or mapped because they contain high GC-content and/or low complexity regions,and complicated pseudogenes,such as the genes encoding xenobiotic metabolizing enzymes and transporters (XMETs).The genetic variants in XMET genes are critical to predicate interindividual variability in drug efficacy,drug safety and susceptibility to environmental toxicity.We summarized and discussed challenges,wet-lab methods,and bioinformatics algorithms in sequencing 'complex' XMET genes,which may provide insightful information in the application of NGS technology for implementation in toxicogenomics and pharmacogenomics. | Yaqiong Jin Geng Chen Wenming Xiao Huixiao Hong Joshua Xu Yongli Guo Wenzhong Xiao Tieliu Shi Leming Shi Weida Tong Baitang Ning | 2019 | Science China(Life Sciences)2019，62，7： | 1 |
| 20 | Protective Effects of Overexpression TCR Vβ5.2-HSP70 and TCR Vβ8.2-HSP70 against Collagen-Induced Arthritis in Rats显示文摘Collagen-induced arthritis(CIA)is an animal model,which closely resembles human rheumatoid arthritis(RA)in pathogenesis and pathology.Evidence suggests that the inhibition of T lymphocytes or their functions can alleviate the progression of arthritis.So the administration of arthritogenic T cell receptor(TCR)variable region peptide or DNA vaccines encoding pathogenic TCR Vβvariable region may provide useful information for designing specific immunotherapies against autoimmune diseases.Heat shock proteins(HSPs)have the function of raising antigenic immunogenicity and HSP70 has a protective effect against arthritis.We previously demonstrated the presence of pathogenic predominant T cell receptor Vβ5.2 and Vβ8.2 clonotypes in the joints of CIA rats.In this study,we constructed the recombinant eukaryotic expression vectors pTARGET-TCR Vβ5.2/8.2-HSP70,and evaluated their protective effects on CIA rats.Protective effects were observed in CIA rats by injecting these recombinant DNA vaccines,which could alleviate arthritis index,decrease the levels of IFN-γand anti-CII antibody in serum,and increase the levels of IL-4.Pathological changes were not as serious as those observed in control CIA rats.The rat injected with two combined vaccines showed better protective effects than CIA rats administered with individual vaccine.These results showed that recombinant DNA vaccines pTARGET-TCR Vβ5.2-HSP70 and pTARGET-TCR Vβ8.2-HSP70 could significantly alleviate the arthritic symptoms of CIA rats,and better protective effects could be achieved if these two vaccines were used in combination. | Jing Xiao Shentao Li Wei Wang Yun Li Wenming Zhao | 2007 | Cellular & Molecular Immunology2007，4，6： | 1 |
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