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| 1 | A draft sequence of the rice (Oryza sativa ssp. indica) genome显示文摘The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a 'whole genome shotgun' approach, we have pro-duced a draft rice genome sequence of Oryza sativa ssp. in-dica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from an indica variant cultivar 93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEM-BLER, a custom-designed software package | YU Jun, HU Songnian, WANG Jun,LI Songgang WONG Ka-Shu Gane, LIU Bin,DENG Yajun, DAI Li, ZHOU Yan,ZHANG Xiuqing, CAO Mengliang, LIU Jing,SUN Jiandong , TANG Jiabin, CHEN Yanjiong,HUANG Xiaobing, LIN Wei, YE Chen, TONG Wei,CONG Lijuan, GENG Jianing, HAN Yujun, LI Lin,LI Wei, HU Guangqiang, HUANG Xiangang,LI Wenjie, LI Jian, LIU Zhanwei, LI Long,LIU Jianping, Ql Qiuhui, LIU Jinsong, LI Li,WANG Xuegang, LU Hong, WU Tingling,ZHU Miao, Nl Peixiang, HAN Hua, DONG Wei,REN Xiaoyu, FENG Xiaoli, GUI Peng,LI Xianran, WANG Hao, XU Xin, ZHAI Wenxue,XU Zhao, ZHANG Jinsong, HE Sijie,ZHANG Jianguo, XU Jichen, ZHANG Kunlin,ZHENG Xianwu, DONG Jianhai, ZENG Wanyong,TAO Lin, CHEN Xuewei, HE Jun, LIU Daofeng,TIAN Wei, TIAN Chaoguang, XIA Hongai,LI Gang, GAO Hui, LI Ping, CHEN Wei ,WANG Xudong, ZHANG Yong, HU Jianfei,WANG Jing, LIU Song, YANG Jian,ZHANG Guangyu, XIONG Yuqing, LI Zhijie,MAO Long, ZHOU Chengshu, ZHU Zhen,CHEN Runsheng, HAO Bailin,ZHENG Weimou, CHEN Shouyi, QUO Wei,LI Guojie, LIU Siqi, HUANG Guyang,TAO Ming, WANG Jian, ZHU Lihuang,YUAN Longping& YANG HuanmingBeijing Genomics Institute/Center of Genomics & Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China Hangzhou Genomics Institute/Institute of Bioinformatics of Zhejiang University/Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China Institute of Genetics, Chinese Academy of Sciences, Beijing 100101, China National Hybrid Rice R & D Center, Changsha 410125, China Laboratory of Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China College of Life Sciences, Peking University, Beijing 100871, China Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 1Q0080, China Digital China Ltd., Beijing 100080, China Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China Medical College, Xi’an Jiaotong University, Xi’an 710061, ChinaThese authors contributed equally to this work.Corresponding author.Corresponden | 2001 | Chinese Science Bulletin2001，46，23： | 6 |
| 2 | Regulation of cellular senescence by the essential caveolar component PTRF/Cavin-1显示文摘聚合酶我和抄本版本因素(PTRF,也作为 Cavin-1 知道) 是在 caveolae 的生物的续生说和功能的一个必要部件。这里,我们证明那 PTRF 表情在衰老的人的成纤维细胞被增加。重要地, PTRF 的 overexpression 导致了细胞的老朽特征的特征,而减少的 PTRF 表示扩大了细胞的 replicative lifespan。有趣地,我们在细胞的老朽期间首先发现那 PTRF 局部性到年轻、静止的 WI-38 人的成纤维细胞,而是 translocated 的原子核到 cytosol 和血浆膜。而且,显微镜的分析表明了的电子 caveolar 结构在的一个增加的数字衰老并且 PTRF-transfected WI-38 房间。我们的数据建议在细胞的老朽的 PTRF 的角色依赖于它指向到有 caveolin-1 的 caveolae 和它的相互作用,它看起来被 PTRF 的 phosphorylation 调整。一起拿,我们的调查结果作为通过 p53/p21 和 caveolar 小径行动的细胞的老朽的一个新奇管理者识别 PTRF。 | Lin Bai Xiaoli Deng Juanjuan Li Miao Wang Qian Li Wei An Deli A Yu-Sheng Cong | 2011 | Cell Research2011，21，7： | 5 |
| 3 | Puromycin A, B and C, cryptic nucleosides identified from Streptomyces alboniger NRRL B-1832 by PPtase-based activation显示文摘Natural product discovery is pivot for drug development,however,this endeavor is often challenged by the wide inactivation or silence of natural products biosynthetic pathways.We recently developed a highly efficient approach to activate cryptic/silenced biosynthetic pathways through augmentation of the phosphopantetheinylation of carrier proteins.By applying this approach in the Streptomyces alboniger NRRL B-1832,we herein identified three cryptic nucleosides products,including one known puromycin A and two new derivatives(puromycin B and C).The biosynthesis of these products doesn't require the involvement of carrier protein,indicating the phosphopantetheinyl transferase(PPtase)indeed plays a fundamental regulatory role in metabolites biosynthesis.These results demonstrate that the PPtasebased approach have a much broader effective scope than the previously assumed carrier proteininvolving pathways,which will benefit future natural products discovery and biosynthetic studies. | Xiaoli Yan Benyin Zhang Wenya Tian Qi Dai Xiaoqin Zheng Ke Hu Xinxin Liu Zixin Deng Xudong Qu | 2018 | Synthetic and Systems Biotechnology2018，3，1： | 3 |
| 4 | Scanning for signatures of geographically restricted selection based on population genomics analysis显示文摘Natural selection, as the driving force of human evolution, has direct impact on population differentiation. However, it is still unclear to what extent the genetic differentiation has been caused by natural selection. To explore this question, we performed a genome-wide scan with single nucleotide polymorphism (SNP) data from the International HapMap Project. Single locus FST analysis was applied to assess the frequency difference among populations in autosomes. Based on the empirical distribution of FST, we identified 12669 SNPs correlating to population differentiation and 1853 candidate genes subjected to geographic restricted natural selection. Further interpretation of gene ontogeny revealed 121 categories of biological process with the enrichments of candidate genes. Our results suggest that natural selection may play an important role in human population differentiation. In addition, our analysis provides new clues as well as research methods for our understanding of population differentiation and natural selection. | DENG LiBin TANG XiaoLi KANG Jian WANG QingYun ZENG ChangQing | 2007 | Chinese Science Bulletin2007，52，19： | 3 |
| 5 | Characterization of the imprinting and expression patterns of ZAG2 in maize endosperm and embryo显示文摘ZAG2 has been identified as a maternally expressed imprinted gene in maize endosperm.Our study revealed that paternally inherited ZAG2 alleles were imprinted in maize endosperm and embryo at 14 days after pollination(DAP), and consistently imprinted in endosperm at 10, 12, 16, 18, 20, 22, 24, 26, and 28 DAP in reciprocal crosses between B73 and Mo17. ZAG2 alleles were also imprinted in reciprocal crosses between Zheng 58 and Chang7-2 and between Huang C and 178. ZAG2 alleles exhibited differential imprinting in hybrids of 178 × Huang C and B73 × Mo17, while in other hybrids ZAG2 alleles exhibited binary imprinting. The tissue-specific expression pattern of ZAG2 showed that ZAG2 was expressed at a high level in immature ears, suggesting that ZAG2 plays important roles in not only kernel but ear development. | Chaoxian Liu Jiuguang Wang Xiupeng Mei Xiaojing Deng Tingting Yu Xiaoli Liu Guoqiang Wang Zhizhai Liu Yilin Cai | 2015 | The Crop Journal2015，3，1： | 3 |
| 6 | Nampt is involved in DNA double-strand break repair显示文摘DNA double-strand break(DSB) is the most severe form of DNA damage,which is repaired mainly through high-fidelity homologous recombination(HR) or error-prone non-homologous end joining(NHEJ).Defects in the DNA damage response lead to genomic instability and ultimately predispose organs to cancer.Nicotinamide phosphoribosyltransferase(Nampt),which is involved in nicotinamide adenine dinucleotide metabolism,is overexpressed in a variety of tumors.In this report,we found that Nampt physically associated with CtIP and DNA-PKcs/Ku80,which are key factors in HR and NHEJ,respectively.Depletion of Nampt by small interfering RNA(siRNA) led to defective NHEJ-mediated DSB repair and enhanced HR-mediated repair.Furthermore,the inhibition of Nampt expression promoted proliferation of cancer cells and normal human fibroblasts and decreased β-galactosidase staining,indicating a delay in the onset of cellular senescence in normal human fibroblasts.Taken together,our results suggest that Nampt is a suppressor of HR-mediated DSB repair and an enhancer of NHEJ-mediated DSB repair,contributing to the acceleration of cellular senescence. | Bingtao Zhu Xiaoli Deng Yifan Sun Lin Bai Zhikai Xiahou Yusheng Cong Xingzhi Xu | 2012 | Chinese Journal of Cancer2012，31，8： | 2 |
| 7 | Inhomogeneous deformation of {111} grain in cold rolled tantalum显示文摘The microstructures of {111} grain were characterized in detailed and systematically investigated with the aid of electron backscatter diffraction(EBSD) and transmission electron microscope(TEM). The stored energy in different regions in the grain was evaluated by the band contrast values collected from EBSD. The results show that the distribution of energy is inhomogeneous through the grain. Especially,the regions containing the least and the largest energy were extracted from the EBSD data, and then quantitatively analyzed based on the misorientation and Schmid factor. Many peaks with large misorientation appeared in the region containing larger energy, and these peaks represent the existences of micro-bands and micro-shear bands in {111} grain. The results of Schmid factor suggest that the region containing larger energy is prone to deforming ahead of the region with less stored energy, implying the more serious subdivision of the microstructure of region with larger stored energy. | Yahui Liu Shifeng Liu Chao Deng Haiyang Fan Xiaoli Yuan Qing Liu | 2018 | Journal of Materials Science & Technology2018，34，11： | 2 |
| 8 | Novel SFTSV Phylogeny Reveals New Reassortment Events and Migration Routes显示文摘Severe fever with thrombocytopenia syndrome virus(SFTSV),the causative agent of a febrile human disease,was first identified from central and eastern provinces in China,and later in Japan and South Korea.Hubei Province is one of the major SFTS epidemic areas in the central part of China.This study reported the isolation of 11 new SFTSV strains from patients in Hubei Province collected in 2017.Extensive phylogenetic analyses were conducted based on the complete coding sequences of SFTSV segments including the new strains.It was suggested that five different SFTSV genotypes were circulating in Hubei,and 15 reassortment patterns and migration pathways correlated with each genotype were identified,which was more than previously recognized.Hubei Province was more involved in the evolutionary events of SFTSV than that previously thought in which the evolutionary events of SFTSV were reported to be independent from those in other epidemic regions.Further divergence of SFTSV strains was suggested by pairwise comparison of SFTSV sequences from each genotype and sequence identity normalized to representative strain in genotype C1.Subsequently,amino acid variations specific for genotype(s),strain(s),or cluster(s)were inspected,which may be related to differential biological activity of SFTSV strains/genotypes.In conclusion,we analyzed the current status of SFTSV phylogeny in Hubei Province and discussed the possible events correlated to SFTSV evolution.It provided an in-depth insight into SFTSV evolution,raising concerns for the use of proper SFTSV strains in future studies. | Xiaoli Wu Mingyue Li Yanfang Zhang Boyun Liang Junming Shi Yaohui Fang Zhengyuan Su Mengmeng Li Wenjing Zhang Ling Xu Jun Wang Qiaoli Wu Shuang Tang Hualin Wang Tao Zhang Cheng Peng Xin Zheng Fei Deng Shu Shen | 2021 | Virologica Sinica2021，36，2： | 2 |
| 9 | Engineering and modification of microbial chassis for systems and synthetic biology显示文摘Engineering and modifying synthetic microbial chassis is one of the best ways not only to unravel the fundamental principles of life but also to enhance applications in the health,medicine,agricultural,veterinary,and food industries.The two primary strategies for constructing a microbial chassis are the top-down approach(genome reduction)and the bottom-up approach(genome synthesis).Research programs on this topic have been funded in several countries.The‘Minimum genome factory’(MGF)project was launched in 2001 in Japan with the goal of constructing microorganisms with smaller genomes for industrial use.One of the best examples of the results of this project is E.coli MGF-01,which has a reduced-genome size and exhibits better growth and higher threonine production characteristics than the parental strain[1].The‘cell factory’project was carried out from 1998 to 2002 in the Fifth Framework Program of the EU(European Union),which tried to comprehensively understand microorganisms used in the application field.One of the outstanding results of this project was the elucidation of proteins secreted by Bacillus subtilis,which was summarized as the‘secretome’[2].The GTL(Genomes to Life)program began in 2002 in the United States.In this program,researchers aimed to create artificial cells both in silico and in vitro,such as the successful design and synthesis of a minimal bacterial genome by John Craig Venter's group[3].This review provides an update on recent advances in engineering,modification and application of synthetic microbial chassis,with particular emphasis on the value of learning about chassis as a way to better understand life and improve applications. | Haotian Chi Xiaoli Wang Yue Shao Ying Qin Zixin Deng Lianrong Wang Shi Chen | 2019 | Synthetic and Systems Biotechnology2019，4，1： | 2 |
| 10 | Coastal Gravity Anomalies from Retracked Geosat/GM Altimetry: Improvement, Limitation and the Role of Airborne Gravity Data显示文摘 | Cheinway Hwang Jinyun Guo Xiaoli Deng Hsin-Ying Hsu Yuting Liu | 2006 | Journal of Geodesy2006，，4： | 1 |
| 11 | Coastal Gravity Anomalies from Retraeked Geosat GM A1- timetry: Improvement, Limitation and the Role of Airborne Gravity Data 显示文摘 | Hwang C Guo Jinyun Deng Xiaoli | 2006 | Journal of Geodesy2006，80，4： | 1 |
| 12 | Pro-inflammatory effects of a litchi protein extract in murine RAW264.7 macrophages显示文摘It has been observed that the consumption of litchi often causes symptoms characterized by itching or sore throat,gum swelling,oral cavity ulcers and even fever and inflammation,which significantly impair the quality of life of a large population.Using the RAW264.7 cell line,a step-by-step strategy was used to screen for the components in litchi fruits that elicited adverse reactions.The adverse reaction fractions were identified by mass spectrometry and analyzed using the SMART program,and a sequence alignment of the homologous proteins was performed.MTT tests were used to determine the cytotoxicity of a litchi protein extract in RAW264.7 macrophages,and real-time PCR was applied to analyze the expression of inflammatory genes in the RAW264.7 cells treated with lipopolysaccharide or the litchi protein extract.The results showed that the litchi water-soluble protein extract could increase the production of the pro-inflammatory mediators IL-1β,iNOS and COX-2,and the anti-inflammatory mediator HO-1 in the RAW264.7 cell line.The 14-3-3-like proteins GF14 lambda,GF14 omega and GF14 upsilon were likely the candidate proteins that caused the adverse effects. | Xiaoli Wang Xiaorong Hu Huiqing Yan Zhaocheng Ma Xiuxin Deng | 2016 | Horticulture Research2016，3，1： | 1 |
| 13 | Experiment and modeling of uniaxial tension fatigue performances for filled natural rubbers显示文摘 | SHANGGUAN Wenbin WANG Xiaoli DENG Jianxiang | 2014 | Materials & Design2014，58，： | 1 |
| 14 | Verification of an independent dose calculation method for portal-specific QA of proton and carbon ion beams显示文摘Objective:To verify the accuracy of an independent dose calculation method,as incorporated into an in-house developed treatment planning system(TPS),for performing quality assurance of dose distributions delivered to a water phantom planned by a clinical TPS.Methods:A Monte Carlo based track repeating algorithm was incorporated into an in-house treatment planning system for proton and carbon ion beams.Calculations were performed in a flat water phantom for both a traditional pencil beam algorithm and a new Monte Carlo algorithm,and then compared to measurements made at multiple depths with a 2D ionization array for 44 patient portals.The comparisons utilized a Gamma analysis.Results:A total of 124 measurements were performed for proton and carbon ion patient portals.Using a small Gamma criteria of 2%/2 mm,an average of 93%and 97%of measurement points passed for each portal for pencil beam and Monte Carlo calculations,respectively.The passing rate was substantially higher for Monte Carlo calculations than for pencil beam calculations for portals that used a range shifter.Conclusions:The implemented independent method has been verified against measurements.The high passing rate with small tolerances leads to the possibility of reducing the number of required quality assurance measurements. | Michael F.Moyers Qianxia Wang Yu Deng Hongliang Chen Zhi Chen Xiaoli Liu Nicki Schlegel Jie Li Zhuangming Shen James Lin Pablo Yepes | 2022 | Radiation Medicine and Protection2022，3，3： | 1 |
| 15 | Seasonal re- sponses of soil respiration to elevated CO2 and N addition in young subtropical forest ecosystems in southern China 显示文摘 | Deng Qi Cheng Xiaoli Zhou Guoyi | 2013 | Ecological Engineering2013，61，： | 1 |
| 16 | Discrimination of varieties of tea using near infrared spectroscopy by principal component analysis and BP model显示文摘 | HE Yong LI Xiaoli Deng Xunfei | 2006 | Journal of Food Engineering2006，79，： | 1 |
| 17 | Discrimination of varieties of tea using near infrared spectroscopy by principal component analysis and BP model显示文摘 | Yong He Xiaoli Li Xunfei Deng | 2006 | Journal of Food Engineering2006，，4： | 1 |
| 18 | Coastal Gravity Anomalies from Retraeked Geosat/GM Altimetry: Improvement, Limitation and the Role of Airborne Gravity Data显示文摘 | HWANG Cheinway GUO Jinyun DENG Xiaoli | 2006 | Journal of Geodesy2006，80，4： | 1 |
| 19 | Coastal Gravity Anomalies from Retracked Geosat/GM Altime- try:Improvement, Limitation and the Role of Airborne Gravity Data 显示文摘 | HWANG CHEINWAY GUO JINYUN DENG XIAOLI | 2006 | Journal of Geodesy2006，80，4： | 1 |
| 20 | Breastfeeding, previous Epstein-Barr virus infection, Enterovirus 71 infection, and rural residence are associated with the severity of hand, foot, and mouth disease显示文摘 | Yaping Li Shuangsuo Dang Huiling Deng Wenjun Wang Xiaoli Jia Ning Gao Mei Li Jun Wang | 2013 | European Journal of Pediatrics2013，，5： | 1 |
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