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| 1 | 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 |
| 2 | 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 |
| 3 | Hydrothermal Dolomite in the Upper Sinian (Upper Proterozoic) Dengying Formation, East Sichuan Basin, China显示文摘Hydrothermal Dolomite(HTD) is present in the Upper Sinian(Upper Proterozoic) Dengying Formation, east Sichuan Basin, China. The strata are comprised by primary dolomite. The HTD has various textures, including zebra dolomite, subhorizontal sheet-like cavities filled by saddle dolomite and breccias cemented by saddle dolomites as well occur as a fill of veins and fractures. Also co-occur MVT type lead-zinc ores in the study area. The δ13C and δ18O isotopes of HTD in the Upper Sinian Dengying Formation are lighter than those of the host rocks, while 87Sr/86 Sr is higher. The apparent difference in carbon, oxygen and strontium isotopes, especially the large difference in 87Sr/86 Sr isotopes ratio indicate crystallization from hot basinal and/or hydrothermal fluids. Saddle dolomite was precipitated at temperatures of 270-320°C. The diagenetic parasequences of mineral assemblage deposited in the Dengying Formation are:(1) dolomite host rock →sphalerite-galena-barite-fluorite;(2) dolomite host rock →saddle dolomite →quartz;(3) dolomite host rock → saddle dolomite→bitumen;(4) dolomite host rock → saddle dolomite → barite. The mean chemical composition of the host dolomite matrix and HTD didn't change much during hydrothermal process. The fluids forming the HTDs in the Dengying Formation were mixtures of freshwater from the unconformity at the top of Sinian, fluids from diagenetic compaction and hydrocarbon generation & expulsion from the Lower Cambrian Niutitang Formation mudstones or the Doushantuo Formation silty mudstones, and hydrothermal fluids from the basement. The hydrocarbon reservoirs associated with the HTD were mostly controlled by the basement faults and fractures and karsting processes at the unconformity separating Sinian and Cambrian strata. The hydrocarbon storage spaces of HTD included dissolved cavities and intercrystalline pores. Dissolution cavities are extensive at the top of Dengying Formation, up to about 46 m below the unconformity between Sinian and Cambrian and were generated mainly during karstification. Hydrothermal alteration enhanced the reservoir property of the Dengying Formation dolomites with 3%-5% increase in porosity. No agreement has been reached why zebra dolomite occurs only in the Upper Sinian strata, which would indicate that HTD mineralization occurred during two different periods, each of them related to major extensional tectonic event. The early one related to the Xingkai taphrogenesis(Z2-?1)and the later one to the Emei taphrogenesis(D2-T2). But, all the data from saddle dolomite suggest that the predominant crystallization occurred during the latter event. | LIU Shugen HUANG Wenming JANSA Luba F. WANG Guozhi SONG Guangyong ZHANG Changjun SUN Wei MA Wenxin | 2014 | Acta Geologica Sinica(English Edition)2014，88，5： | 11 |
| 4 | 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 |
| 5 | A glucocorticoid amplifies IL-2-induced selective expansion of CD4^+CD25^+FOXP3^+ regulatory T cells in vivo and suppresses graft-versus-host disease after allogeneic lymphocyte transplantation显示文摘规章的 T (Treg ) 房间是不仅阻止 autoimmunity,而且控制大量 T 房间依赖者免疫者回答的 T 房间的 subpopulation。Glucocorticoid 处理(dexamethasone,或 Dex ) 被报导了放大在 Treg 房间的 vivo 扩大选择的 IL-2-mediated。我们同时在一个鼠科的 allogeneic 淋巴细胞移植模型予施主以 Dex 和 IL-2 在接枝扩展功能的镇压 CD4+CD25+FOXP3+ T 房间并且提起规章的 T 房间 / 受动器 T 房间(Treg/Teff ) 比率阻止 graft-versus-host 疾病(GVHD ) 。在有 Dex (5 mg/kg/day ) 和为 3 天的 IL-2 (300,000 IU/mouse/day ) 的施主的联合处理以后,接枝受到流动 cytometric 分析,并且移植 812 个星期从男 C57BL/6 老鼠被执行到女 BALB/c 老鼠。结果显示出 Dex 的那个短期的同时的政府, IL-2 显著地在鼠科的怒气扩展了功能的镇压 CD4+CD25+FOXP3+ T 房间。在这个鼠科的 allogeneic 移植模型,从有 Dex 和 IL-2 预告的处理的施主的接枝比为控制组为接受者导致了一更长的幸存时间(中部的幸存时间 > 60 白天对 12 白天, P = 0.0002 ) 。Treg/Teff 的比率也显著地增加了(0. | Yanhui Xie Min Wu Runhua Song Jiexian Ma Yi Shi Wenming Qin Youxin Jin | 2009 | Acta Biochimica et Biophysica Sinica2009，41，9： | 3 |
| 6 | Surface composites fabricated by vacuum infiltration casting technique显示文摘Alumina (Al2O3) particles reinforced copper matrix surface composites were fabricated on the bronze substrate using the vacuum infiltration casting technique. Three cases were obtained in the vacuum infiltration casting technique: no infiltration, partial infiltration and full infiltration (the thickness of preforms do not exceed 3.5 mm). The reason of no infiltration is that the vacuum degree is not enough so that the force acting on the liquid metal is lower than the resistance due to the surface tension. Partial infil- tration is because of somewhat lower vacuum degree and pouring temperature. Full desired infiltration is on account of suitable in- filtration casting conditions, such as vacuum degree, pouring temperature, grain size and preheating temperature of the preform. The most important factor of affecting formation of surface composites is the vacuum degree, then pouring temperature and particle size. The infiltration mechanism was discussed on the bases of different processing conditions. The surface composite up to 3.5 mm in thickness with uniformly distributed Al2O3 particles could be fabricated via the vacuum infiltration casting technique. | Guirong Yang Yuan Hao Wenming Song Jinjun Lii Ying Ma | 2005 | Journal of University of Science and Technology Beijing2005，12，5： | 3 |
| 7 | Molecular cloning and expression patterns of the cholesterol side chain cleavage enzyme(CYP11A1) gene during the reproductive cycle in goose(Anas cygnoides)显示文摘Background: CYP11A1, a gene belonging to the family 11 of cytochrome P450, encodes a crucial steroidogenic enzyme that catalyzes the initial step in the production of all classes of steroids. Many studies show that CYP11A1 plays a role in ovary function. However, the role of CYP11A1 in goose reproductive cycle remains largely unknown.Results: In this study, full-length CYP11A1 c DNA of Zhedong goose was obtained using reverse transcription polymerase chain reaction(RT-PCR) and rapid amplification of c DNA ends(RACE). The c DNA consisted of a 96-base pair(bp) 5′untranslated region(UTR), a 179-bp 3′UTR and a 1509-bp open reading frame. The open reading frame encodes a putative 503 amino acid protein that shares high homology with CYP11A1 of other birds. The amino acid sequence possesses conserved domains of the P450 superfamily, which include the steroid-binding domain and the heme-binding region. Real-time quantitative polymerase chain reaction(q PCR) analysis revealed CYP11A1 mR NA was expressed ubiquitously in every Zhedong goose tissue analyzed, including the heart, liver, glandular stomach,lung, spleen, kidney, intestinum tenue, intestinum crassum, cerebrum, cerebellum, muscle, oviduct, pituitary,hypothalamus and ovary.. The relatively low levels of CYP11A1 m RNA were detected in pituitary, ovary and oviduct tissues at ovulation when compared with levels at oviposition. Interestingly, higher expression was observed in ovary and oviduct tissues during brooding. Lastly, higher m RNA expression of Yangzhou geese was detected during the ovulation period than that of Zhedong geese.Conclusions: Our findings reveal the sequence characterization and expression patterns of the CYP11A1 gene during the goose reproductive cycle, which may provides correlative evidence that CYP11A1 expression is important in reproduction activity. | Qi Xu Yadong Song Yang Chen Ran Liu Yang Zhang Yang Li Zhengyang Huang Wenming Zhao Guobin Chang Guohong Chen | 2016 | Journal of Animal Science and Biotechnology2016，7，2： | 2 |
| 8 | Responses of Seed Yield and Economic Benefit of Winter Oilseed Rape(Brassica napus L.) to Different NPK Ratio and Dose显示文摘Field experiments were conducted during 2008-2010 to investigate the effects of NPK fertilization on seed yield and economic benefit of a new hybrid cultivar of winter oilseed rape(Brassica napus L.)- Xiangzayou763,and to determine the optimum NPK ratio and dose in Hunan,China.The results showed that NPK ratio(1:0.50:0.50) with 180 kg/hm2 N,90 kg/hm^2 P_2O_5 and 90 kg/hm^2 K_2O was the optimum combination for the highest seed yield(2 231.13 kg/hm2) and economic benefit(9 816.97 Yuan/hm^2),of which 1 641.23 Yuan/hm^2 being set for fertilizer investment(VCR=4.11).Besides,the effects of N,P and K fertilizers on seed yield and oil production of winter oilseed rape were not identical.N had the greatest effect on plant growth of winter oilseed rape,followed by P and K.Total leaf number,green leaf number,leaf length and width,rhizome diameter,branch number,dry weight per plant and other agronomic characters in high N treatments were higher than those in low N treatments.By correlation and path analysis of yield components,the contribution rate to seed yield was found:effective silique number per plant>seed number per silique>1 000-seed weight. | Yingzi WANG Chang TIAN Xuan ZHOU Wenming WANG Jianwei PENG Zhenhua ZHANG Haixing SONG Chunyun GUAN | 2015 | Agricultural Science & Technology2015，16，11： | 2 |
| 9 | Feasibility Study of Aluminum Hydroxide Sol as Adjuvant to Prepare Stable Vaccine Using Newcastle Disease Virus as a Model显示文摘Aluminum hydroxide sol (consisting of aluminum hydroxide nano-particles) prepared by a hydrothermal method was used as nano-aluminum adjuvant adsorbed the inactived Newcastle disease virus (NDV). The zeta potential of aluminum hydroxide colloidal particles,the inactivated NDV and the nano-aluminum adjuvant NDV are +48.16 mV,?13.8 mV and +39.97 mV,respec-tively. The nano-aluminum adjuvant vaccine was transparent and stable without precipitate,whereas the conventional aluminum ad-juvant vaccine was turbid and a white precipitate was visible soon. The hemagglutination inhibition (HI) titers of the nano-aluminum adjuvant group were generally higher than those of the conventional aluminum group except the titer on day 29. The results show that the nano-aluminum adjuvant has better stability and higher levels of antibodies for a longer time than the conventional aluminum adjuvant. | SONG Meirong LI Xinsheng GAO Wenming FANG Shaoming CUI Baoan | 2011 | Wuhan University Journal of Natural Sciences2011，16，1： | 1 |
| 10 | Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters显示文摘A novel RNA virus,the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),is responsible for the ongoing outbreak of coronavirus disease 2019(COVID-19).Population genetic analysis could be useful for investigating the origin and evolutionary dynamics of COVID-19.However,due to extensive sampling bias and existence of infection clusters during the epidemic spread,direct applications of existing approaches can lead to biased parameter estimations and data misinterpretation.In this study,we first present robust estimator for the time to the most recent common ancestor(TMRCA)and the mutation rate,and then apply the approach to analyze 12,909 genomic sequences of SARS-CoV-2.The mutation rate is inferred to be 8.69×10^(−4) per site per year with a 95%confidence interval(CI)of[8.61×10^(−4),8.77×10^(−4)],and the TMRCA of the samples inferred to be Nov 28,2019 with a 95%CI of[Oct 20,2019,Dec 9,2019].The results indicate that COVID-19 might originate earlier than and outside of Wuhan Seafood Market.We further demonstrate that genetic polymorphism patterns,including the enrichment of specific haplotypes and the temporal allele frequency trajectories generated from infection clusters,are similar to those caused by evolutionary forces such as natural selection.Our results show that population genetic methods need to be developed to efficiently detangle the effects of sampling bias and infection clusters to gain insights into the evolutionary mechanism of SARS-CoV-2.Software for implementing VirusMuT can be downloaded at https://bigd.big.ac.cn/biocode/tools/BT007081. | Qi Liu Shilei Zhao Cheng-Min Shi Shuhui Song Sihui Zhu Yankai Su Wenming Zhao Mingkun Li Yiming Bao Yongbiao Xue Hua Chen | 2020 | Genomics, Proteomics & Bioinformatics2020，18，6： | 1 |
| 11 | An investigation of the structure and properties of infiltrated layer on the surface of copper alloy 显示文摘 | YANG Guirong HAO Yuan SONG Wenming | 2005 | Material Science and Engineering A2005，399，12： | 1 |
| 12 | Micron-to nano-pore characteristics in the shale of Longmaxi Formation,southeast Sichuan Basin显示文摘For shale of Lower Silurian Longmaxi Formation in Chongqing,southeast Sichuan Basin,characteristics of micro-nano pores in marine shale reservoirs were well studies by means of Field-Emission Scanning Electron Microscope and Low-temperature Low-pressure Adsorption Experiment of CO_(2)and N_(2).Results showed that six types of pore were developed in the shale of Longmaxi Formation,i.e.,organic pores,intergranular pores,intragranular pores,intercrystalline pores,dissolution pores and microfractures,among which the organic pores and intragranular pores in interlayers of clay minerals were most developed,and a plenty of dissolution pores were also well developed because of high thermal evolution degree.BET specific surface area of the shale in Longmaxi Formation ranged from 3.5 to 18.1 m^(2)/g,BJH total pore volume was from 0.00234 to 0.01338 cm^(3)/g,DA specific surface area of micropores vaired from 1.3 to 7.3 m^(2)/g,and DA pore volume ranged from 0.00052 to 0.00273 cm^(3)/g.The specific surface area of micropores in the shale accounted for 23.1%-80.2%of total specific surface area with an average of 50.3%,and the pore volume of micropores accounted for 12.1%-48.5%of total pore volume with an average of 32.3%.Micropore was the main storage space in shale reservoir for methane adsorption,that because capacities of specific surface area provided by micropores were considerably greater than those provided by mesopores and macropores.Pore size distribution of the shale was complex,and multiple different peaks occurred in the pore size curves,showing two or three peaks in the range from 0 to 100 nm and four peaks occasionally.TOC had a good linear relationship with pore structure parameters of micropores,mesopores t macropores and total pores in the shale,indicating that TOC was the most important control factor for micron-to nano-pore structure in the shale.After normalization of pore structure parameters to TOC,the pore structure parameters of total pores and mesopores t macropores,had positive linear relationships with content of clay minerals but negative linear relationships with content of brittle minerals,indicating that clay minerals and brittle minerals mainly controlled development of mesopores and macropores in the shale. | Wenming Ji Yan Song Zhenxue Jiang Mianmo Meng Qingxin Liu Fenglin Gao | 2017 | Petroleum Research2017，2，2： | 1 |
| 13 | An investigation of the structure and properties of infiltrated layer on the surface of copper alloy 显示文摘 | Yang Guirong Yuan H Song Wenming | 2005 | Materials Science and Engineering2005，399，12： | 1 |
| 14 | The high temperature property of Ni/WC infiltrated composite layer on cast iron substrate 显示文摘 | Yang Guirong Song Wenming Ma Ying | 2010 | Advanced Materials Research2010，，97101： | 1 |
| 15 | The research on wear performance at elevated temperature of Ni-based infiltrated layer 显示文摘 | Yang Guirong Zhou You Song Wenming | 2011 | Advanced Materials Research2011，，： | 1 |
| 16 | Surface Com- posites Fabricated by Vacuum Infiltration Casting Technique显示文摘 | Guirong YANG Yuan HAO Wenming SONG | 2006 | Surface Coating and Technology2006，201，12： | 1 |
| 17 | Surface Composite Fabrication Using Fe-based Alloying Powder through Infiltration Casting Technique on Copper Substrate显示文摘 | Guirong YANG Wenming SONG Yuan HAO | 2006 | Material Science and Engineering A2006，419，12： | 1 |
| 18 | Microstructure and Wear Behaviour of Ni-based Surface Coating on Copper Substrate显示文摘 | Wenming SONG Guirong YANG Yuan HAO | 2007 | Wear2007，262，78： | 1 |
| 19 | Three-point bending behavior of surface composite Al2O3/Ni on bronze substrate produced by vacuum infiltration casting显示文摘 | Yang Guirong Song Wenming Jin Junlu | 2008 | Journal of Materials Processing Technology2008，202，13： | 1 |
| 20 | AIM interneurons mediate feeding suppression through the TYRA-2 receptor in C elegans显示文摘 | Jiajun Fu Haining Zhang Wenming Huang Xinyu Zhu Yi Sheng Eli Song Tao Xu | 2018 | Biophysics Reports2018，4，1： | 1 |
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