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| 1 | Efficient and Specific Modifications of the Drosophila Genome by Means of an Easy TALEN Strategy显示文摘技术开发总是是在生物医学的研究驾驶突破的力量之一。自从托马斯·摩根的时间起,一步一步地, Drosophilists 为操作并且机能上地把开发了强大的基因工具为改进这些技术并且开发新技术的果蝇染色体,而是房间仍然大,今天特别作为生物学家开始系统地学习不同模型有机体的功能的 genomics ,包括人,以一种高产量的方式。这里,我们报导,第一次在果蝇,为借助于改进抄写在很高的效率修改果蝇染色体的一个快速、容易、高度特定的方法像使活跃之物的受动器核酸酶(TALEN ) 策略。我们利用了最近发达的单位集会策略装配设计修改黄基因的二特定的 TALEN (在性染色体上) 并且新奇正染色体的基因。TALEN 的 mRNAs 随后被注入果蝇胚胎。从 31.2% 注射 F0 肥沃的苍蝇,我们检测了包含黄基因的可继承的修正。从到可继承的修正的察觉的特定的 TALEN 的建设的全部过程能在一个月以内被完成。在果蝇的这个调停 TALEN 的染色体修正方法的潜在的应用程序被讨论。 | Jiyong Liu Changqing Li Zhongsheng Yu Peng Huang Honggang Wu Chuanxian Wei Nannan Zhu Yan Shen Yixu Chen Bo Zhang Wu-Min Deng Renjie Jiao | 2012 | Journal of Genetics and Genomics2012，39，5： | 43 |
| 2 | Bow-tie topological features of metabolic networks and the functional significance显示文摘Exploring the structural topology of genome-based large-scale metabolic network is essential for in- vestigating possible relations between structure and functionality.Visualization would be helpful for obtaining immediate information about structural organization.In this work,metabolic networks of 75 organisms were investigated from a topological point of view.A spread bow-tie model was proposed to give a clear visualization of the bow-tie structure for metabolic networks.The revealed topological pattern helps to design more efficient algorithm specifically for metabolic networks.This coarse- grained graph also visualizes the vulnerable connections in the network,and thus could have important implication for disease studies and drug target identifications.In addition,analysis on the reciprocal links and main cores in the GSC part of bow-tie also reveals that the bow-tie structure of metabolic networks has its own intrinsic and significant features which are significantly different from those of random networks. | ZHAO Jing TAO Lin YU Hong LUO JianHua CAO ZhiWei LI YiXue | 2007 | Chinese Science Bulletin2007，52，8： | 19 |
| 3 | Comparative profiling of genes and miRNAs expressed in the newborn, young adult, and aged human epididymides显示文摘在通过老化从出生后的开发在 epididymis 调整基因表示理解 transcriptional 因素和 miRNAs 的角色,在新生儿,年轻成年人,和年老的人表示的基因和 miRNAs 的系统的介绍 epididymides 被 cDNA 数组和 miRNA 数组分析分别地执行。新生的人的 epididymis 表示了 fewest mRNAs 但是 miRNAs 的最大的数字而成年、年老的 epididymides 表示了大多数 mRNAs 但是 fewest miRNAs,在 mRNAs 和 miRNA 之间的否定关联在老化期间。由综合分析,一套 miRNA 目标基于 miRNA 和 cDNA 数组被预言。在新生的 epididymis, 127 miRNAs 只或优先地被表示,但是仅仅 3 和 2 miRNAs 分别地在成年、年老的 epididymides 显示出一个充实年龄的表示模式。这研究在 epididymis 在基因表示的复杂规定上为进一步的研究象新卓见和基础一样提供一个基本数据库。 | Jinsong Zhang Qiang Liu Wei Zhang Jianyuan Li Zheng Li Zhongyi Tang Yixue Li Chunsheng Han Susan H. Hall Yonglian Zhang | 2010 | Acta Biochimica et Biophysica Sinica2010，42，2： | 15 |
| 4 | Microvessel changes in the gerbil hippocampus after cerebral ischemia and reperfusion by Buyang Huanwu decoction pretreatment显示文摘Buyang Huanwu decoction(BYHWD) is a classic recipe for the prevention and treatment of ischemic cerebrovascular disease.Gerbils were pretreated with BYHWD,and then subjected to cerebral ischemia and reperfusion.Microvascular changes were determined with laser Doppler monitoring,tannic acid-ferric chloride mordant,and electron microscopy.Results showed that BYHWD pretreatment could enhance the function of hippocampal microvessels,prevent injury,and increase microvasular density and microvasular area density.Thus,these results suggest that BYHWD pretreatment could prevent microvascular occlusion,enhance the capacity of microvascular reperfusion,increase cerebral blood flow,and inhibit neuronal damage,and may be an effective therapy against brain ischemic injury. | Xiaoguang Wu Yixue Li Haixia Liu Yuhua Yin Shumin Zhao Yuanyuan Guo | 2011 | Neural Regeneration Research2011，6，9： | 11 |
| 5 | Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601显示文摘稀释毒力的螺旋体 interrogans serovar Lai 紧张 IPAV 被延长实验室经过从在中国孤立的高度剧毒的祖先的紧张导出。我们学习了 IPAV 的基因变化对病原的 L 经由比较分析使它变为无毒害。interrogans serovar Lai 紧张 56601。IPAV 紧张的完全的染色体顺序决心、使用与作比较,然后修正并且重新注解紧张 56601 的染色体顺序。除了他们的高度类似的 genomic,结构和基因顺序, 33 插入的一个总数, 53 删除和 301 个单个核苷酸的变化(SNV ) 在整个直接影响 101 基因的 IPAV 的染色体被检测,在他们的 5 ′ 的任何一个;在上游的区域或在他们的编码区域以内。在他们之中, 44 功能的基因的多数涉及信号 transduction,压力反应, transmembrane 运输和氮新陈代谢。基于量的液体,层析(LC )-MS/MS 数据揭示了的比较 proteomic 分析在 orthologs 的 1 627 选择的对之中,在 IPAV 的 174 基因拉紧,这是 upregulated,与主要在精力的班上的丰富生产和类脂化合物新陈代谢。相反,在紧张 56601 的 228 基因是 upregulated,与在蛋白质翻译和 DNA 复制 / 修理的范畴充实的多数。 genomic 和 proteomic 途径的联合在批评基因说明了那改变的表情或变化,例如编码 Ser/Thr kinase ,碳饥饿蛋白质 CstA ,夫酸安合成酶,GTP有约束力的蛋白质 BipA , ribonucleotide-diphosphate reductase 和磷酸盐 transporter 的那些,并且在脂蛋白或外部膜蛋白质的翻译侧面的改变是可能的在紧张 IPAV 说明毒力变细。 | Yi Zhong Xiao Chang Xing-Jun Cao Yan Zhang Huajun Zheng Yongzhang Zhu Chengsong Cai Zelin Cui Yunyi Zhang Yuan-Yuan Li Xiu-Gao Jiang Guo-Ping Zhao Shengyue Wang Yixue Li Rong Zeng Xuan Li Xiao-Kui Guo | 2011 | Cell Research2011，21，8： | 10 |
| 6 | Complex networks theory for analyzing metabolic networks显示文摘One of the main tasks of post-genomic informatics is to systematically investigate all mole- cules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of the organism, while networks are appropriate abstract description of all kinds of interactions. In the past few years, great achievement has been made in developing theory of complex networks for revealing the organizing prin- ciples that govern the formation and evolution of various complex biological, technological and social networks. This paper reviews the accomplishments in constructing genome-based metabolic networks and describes how the theory of complex networks is applied to analyze metabolic networks. | ZHAO Jing YU Hong LUO Jianhua CAO Z. W. LI Yixue | 2006 | Chinese Science Bulletin2006，51，13： | 10 |
| 7 | FluxExplorer: A general platform for modeling and analyses of metabolic net-works based on stoichiometry显示文摘Stoichiometry-based analyses of meta- bolic networks have aroused significant interest of systems biology researchers in recent years. It is necessary to develop a more convenient modeling platform on which users can reconstruct their network models using completely graphical operations, and explore them with powerful analyzing modules to get a better understanding of the properties of metabolic systems. Herein, an in silico platform, FluxExplorer, for metabolic modeling and analyses based on stoichiometry has been developed as a publicly available tool for systems biology research. This platform integrates various analytic approaches, in- cluding flux balance analysis, minimization of meta- bolic adjustment, extreme pathways analysis, shadow prices analysis, and singular value decom- position, providing a thorough characterization of the metabolic system. Using a graphic modeling process, metabolic networks can be reconstructed and modi- fied intuitively and conveniently. The inconsistencies of a model with respect to the FBA principles can be proved automatically. In addition, this platform sup- ports systems biology markup language (SBML). FluxExplorer has been applied to rebuild a metabolic network in mammalian mitochondria, producing meaningful results. Generally, it is a powerful and very convenient tool for metabolic network modeling and analysis. | LUO Ruoyu LIAO Sha ZENG Shaoqun LI Yixue LUO Qingming | 2006 | Chinese Science Bulletin2006，51，6： | 6 |
| 8 | Highly efficient base editing in human tripronuclear zygotes显示文摘 | Changyang Zhou Meiling Zhang Yu Wei Yidi Sun Yun Sun Hong Pan Ning Yao Wanxia Zhong Yixue Li Weiping Li3 Hui Yang Zi-jiang Chen | 2017 | Protein & Cell2017，8，10： | 6 |
| 9 | Drosophila RecQ5 is required for efficient SSA repair and suppression of LOH in vivo显示文摘RecQ5 in mammalian cells has been suggested to suppress inappropriate homologous recombination.However,the specific pathway(s)in which it is involved and the underlining mechanism(s)remain poorly understood.We took advantage of genetic tools in Drosophila to investigate how Drosophila RecQ5(dRecQ5)functions in vivo in homologous recombination-mediated double strand break(DSB)repair.We generated null alleles of dRecQ5 using the targeted recombination technique.The mutant animals are homozygous viable,but with growth retardation during development.The mutants are sensitive to both exogenous DSB-inducing treatment,such as gamma-irradiation,and endogenously induced double strand breaks(DSBs)by I-Sce I endonuclease.In the absence of dRecQ5,single strand annealing(SSA)-mediated DSB repair is compromised with compensatory increases in either inter-homologous gene conversion,or non-homologous end joining(NHEJ)when inter-chromosomal homologous sequence is unavailable.Loss of function of dRecQ5 also leads to genome instability in loss of heterozygosity(LOH)assays.Together,our data demonstrate that dRecQ5 functions in SSA-mediated DSB repair to achieve its full efficiency and in suppression of LOH in Drosophila. | Yixu Chen Wen Dui Zhongsheng Yu Changqing Li Jun Ma Renjie Jiao | 2010 | Protein & Cell2010，1，5： | 5 |
| 10 | Prediction and systematic study of protein-protein interaction networks of Leptospira interrogans显示文摘Leptospira interrogans serovar Lai is a pathogenic bacterium that causes a spirochetal zoonosis in humans and some animals. With its complete genome sequence available, it is possible to analyze protein-protein interactions from a whole- genome standpoint. Here we combine four recently developed computational approaches (gene fusion method, gene neighbor method, phylogenetic profiles method, and operon method) to predict protein-pro- tein interaction networks of Leptospira interrogans strain Lai. Through comprehensive analysis on in- teractions among proteins of motility and chemotaxis system, signal transduction, lipopolysaccaride bio- synthesis and a series of proteins related to adhesion and invasion, we provided information for further studying on its pathogenic mechanism. In addition, we also assigned 203 previously uncharacterized proteins with possible functions based on the known functions of its interacting partners. This work is helpful for further investigating L. interrogans strain Lai. | SUN Jingchun XU Jinlin CAO Jianping LIU Qi GUO Xiaokui SHI Tieliu LI Yixue | 2006 | Chinese Science Bulletin2006，51，11： | 3 |
| 11 | Big Biological Data:Challenges and Opportunities显示文摘In‘‘Omics’’era of the life sciences,data is presented in many forms,which represent the information at various levels of bio logical systems,including data about genome,transcriptome epigenome,proteome,metabolome,molecular imaging,molec ular pathways,different population of people and clinical/med ical records.The biological data is big,and its scale has already been well beyond petabyte(PB)even exabyte(EB). | Yixue Li Luonan Chen | 2014 | Genomics, Proteomics & Bioinformatics2014，12，5： | 3 |
| 12 | Subtyping of type A influenza by sequencing the variable regions of HA gene specifically amplified with RT-PCR显示文摘The outbreak of a novel influenza A(H1N1) virus across the globe poses a threat to human health.It is of paramount importance to develop a rapid,reliable and inexpensive diagnostic procedure.Based on the bioinformatic information from public database,primers specific for influenza A virus surface protein haemagglutinin(HA) of several subtypes(including H1,H2,H3,H5,H7 and H9) were designed.Primer-specific PCR products were subjected to sequencing for accurately distinguishing H1 and H3 subtypes from others.This sequencing-based detection method will not only be applied to rapid detection and simultaneous subtype identification of new influenza A virus H1N1,but also provide the strategies to monitor other new types ofinfluenza virus with explosive potential. | YAN An DING GuoHui ZHOU ZhenFeng DONG Hui ZHANG YaKun ZHU Lei HE YunGang ZHANG GuoQing LI YiXue SUN Bing HUANG Zhong LAN Ke JIN Li WANG HongYan WANG XiaoNing YANG Zhong ZHONG Yang DAI JianXin GUO YaJun WANG Hao CHE XiaoYan WU Fan YUAN ZhenGan ZHANG Xi CAO ZhiWei ZHOU XiaoNong ZHOU JiaHai MA ZhiYong TONG GuangZhi ZHAO GuoPing JIN WeiRong XIONG Hui | 2009 | Chinese Science Bulletin2009，54，13： | 3 |
| 13 | The mutation network for the hemagglutinin gene from the novel influenza A (H1N1) virus显示文摘A mutation network for the hemagglutinin gene(HA) of the novel type A(H1N1) influenza virus was constructed.Sequence homology analysis indicated that one HA sequence type from the viruses mainly isolated from Mexico was likely the original type in this epidemic.Based on the 658A and 1408T mutations in HA,the viruses evolving into this epidemic were divided into three categories,the Mexico,the transitional and the New York type.The three groups of viruses presented distinctive clustering features in their geographic distributions. | HE YunGang DING GuoHui BIAN Chao HUANG Zhong LAN Ke SUN Bing WANG XueCai LI YiXue WANG HongYan WANG XiaoNing YANG Zhong ZHONG Yang JIN WeiRong XIONG Hui DAI JianXin GUO YaJun WANG Hao CHE XiaoYan WU Fan YUAN ZhenAn ZHANG Xi CAO ZhiWei ZHOU XiaoNong ZHOU JiaHai MA ZhiYong TONG GuangZhi ZHAO GuoPing JIN Li | 2009 | Chinese Science Bulletin2009，54，13： | 3 |
| 14 | miR-27b synergizes with anticancer drugs via p53 activation and CYPIB1 suppression显示文摘 | Wenjing Mu Chaobo Hu Haibin Zhang Zengqiang Qu Jin Cen Zhixin Qiu Chao Li Haozhen Ren Yixue Li Xianghuo He Xiaolei Shi Lijian Hui | 2015 | Cell Research2015，25，4： | 3 |
| 15 | Overview of SMP-CAIL2020-Argmine:The Interactive Argument-Pair Extraction in Judgement Document Challenge显示文摘In this paper we present the results of the Interactive Argument-Pair Extraction in Judgement Document Challenge held by both the Chinese AI and Law Challenge(CAIL)and the Chinese National Social Media Processing Conference(SMP),and introduce the related data set-SMP-CAIL2020-Argmine.The task challenged participants to choose the correct argument among five candidates proposed by the defense to refute or acknowledge the given argument made by the plaintiff,providing the full context recorded in the judgement documents of both parties.We received entries from 63 competing teams,38 of which scored higher than the provided baseline model(BERT)in the first phase and entered the second phase.The best performing system in the two phases achieved accuracy of 0.856 and 0.905,respectively.In this paper,we will present the results of the competition and a summary of the systems,highlighting commonalities and innovations among participating systems.The SMP-CAIL2020-Argmine data set and baseline modelshave been already released. | Jian Yuan Zhongyu Wei Yixu Gao Wei Chen Yun Song Donghua Zhao Jinglei Ma Zhen Hu Shaokun Zou Donghai Li Xuanjing Huang | 2021 | Data Intelligence2021，3，2： | 3 |
| 16 | Comparative analysis of whole-genome sequences of Streptococcus suis显示文摘The outbreak of Streptococcus suis re-cently in some districts of Sichuan Province in China has caused over 30 deaths and over 200 infections in human beings. In order to study the pathogenicity mechanism and to prevent the bacteria from spreading and infecting human beings and swine, we have annotated and analyzed the genomes of two strains, Streptococcus suis P1/7 and 89-1591 re-spective1y. The whole length of P1/7 is 2.007 Mb, and has 1969 ORFs. In contrast, the partial genome sequence of 89-1591 is 1.98 Mb in length and exists in 177 contigs with 1918 ORFs. Analysis shows that the average lengths of CDSs in two genomes are very close, and the numbers of the homolog ORFs are 1306 between those two strains. Most of the tox-icity factors of the two strains are homologeous, but there are still some significant differences between those two strains. For example, among the 11 genes (cps2A―cps2K) encoding for the capsules in P1/7, 4 (cps2A, 2B, 2I, 2J) are not detected in strain 89-1591. At the same time, the genes encoding EF and Haemolysin in P1/7 are also not found in strain 89-1591. Besides, the genes related to DNA replica-tion, repair and recombination differ from each other significantly and there also exist certain differences among the surface proteins. Those characteristics indicate that those two strains have evolved their ownspecific functions to adapt to the different environ-ments and that the pathogenesis of the two strains is different. We have accumulated comprehensive ge-nomics information for future systematic studies of S. sui. Our results are helpful for disease prevention, vaccine development, as well as drug design for S. suis. | WEI Wu DING Guohui WANG Xiaojing SUN dingchun TU Kang HAO Pei WANG Chuan CAO Zhiwei SHI Tieliu LI Yixue | 2006 | Chinese Science Bulletin2006，51，10： | 2 |
| 17 | Identification of Chinese Materia Medicas in Microscopic Powder Images显示文摘This paper describes an identification system for Chinese Materia Medicas (CMMs) in microscopic powder images.The imaging processing of the microscopic powder image is very complex because of the low contrast,blurry boundaries,overlapping objects,and messy background.Therefore,the object detection must segment the significant microscopic structures from the complex image.The objects are detected in these images using an adaptable interactive method.After identifying the significant microscopic structures,the system identifies 14 features belonging to three main characteristics.These features form a 14-dimensional vector that represents the microscopic structures.The multi-dimensional vector is then analyzed using a feature assignment algorithm that picks the most notable features to construct a decision tree with thresholds.The identification system consists of a coarse classifier based on the decision tree and a fine classifier using similarity measurements to rank the possible results.Tests on 528 images from 24 different kinds of microscopic structures show the system effectiveness and applicability. | Shen Yan Yaoli Li Yixu Song Li Lin Peifa Jia Shaoqing Cai | 2012 | Tsinghua Science and Technology2012，17，2： | 2 |
| 18 | Analysis and application of large-scale protein-protein interaction data sets显示文摘Protein-protein interactions play key roles in cells. Lots of experimental approaches and in silico methods have been developed to identify and predict large-scale pro- tein-protein interactions. However, compared with the tradi- tionally experimental results, the high-throughput pro- tein-protein interaction data often contain the false positives in high probability. In order to fully utilize the large-scale data, it is necessary to develop bioinformatic methods for systematically evaluating those data in order to further im- prove the data reliability and mine biological information. This review summarizes the methodologies of analysis and application of high-throughput protein-protein interaction data, including the evaluation methods, the relationship be- tween protein-protein interaction data and other protein biological information, and their applications in biological study. In addition, this paper also suggests some interesting topics on mining high-throughput protein-protein interaction data. | SUN Jingchun XU Jinlin LI Yixue SHI Tieliu | 2005 | Chinese Science Bulletin2005，50，20： | 2 |
| 19 | Docking and molecular dynamics studies on CYP2D6显示文摘Drug-metabolizing enzymes,also known as cytochrome P450s,are a superfamily of hemoglobin responsible for metabolizing more than 90% clinical drugs.Cytochrome P450 2D6(CYP2D6) is a significant member of cytochrome P450s for the reason of metabolizing about 20% clinical drugs.In this paper,molecular docking and molecular dynamic simulations are used to investi-gate the active site of CYP2D6,roles of essential amino acids within the active site and time-dependent protein energy changes.The results suggest that amino acids Glu216,Asp301,Ser304 and Ala305 in the active site are likely to form hydrogen bonding interactions with substrates;the benzene ring of Phe120 and aromatic ring in the substrates form Π-Π interactions.In addition,molecular dynamics simulations prove that the catalytic conformation of CYP2D6 without ligands can be obtained by their own atomic fluctuations.The impact of ligands on protein system energy and large conformational shift is not very large.Cytochrome P450s is known for their genetic polymorphisms,which will result in severe adverse drug reactions.Ideally,we hope to use mo-lecular modeling to investigate the differences between the substrates of wild-type and mutants while they are bonded with drugs,and predict the drug metabolizing ability of mutants.Reduce the possibility for people taking drugs that they can not metabolize,therefore reduce the rate of adverse drug reactions,and eventually establish a platform of personalized drugs to largely benefit human health. | WANG JingFang ZHANG ChengCheng WEI DongQing LI YiXue | 2010 | Chinese Science Bulletin2010，55，18： | 2 |
| 20 | Analysis of the origin of peak aerosol optical depth in springtime over the Gulf of Tonkin显示文摘By aggregating MODIS(moderate-resolution imaging spectroradiometer) AOD(aerosol optical depth) and OMI(ozone monitoring instrument) UVAI(ultra violet aerosol index)datasets over 2010–2014, it was found that peak aerosol loading in seasonal variation occurred annually in spring over the Gulf of Tonkin(17–23°N, 105–110°E). The vertical structure of the aerosol extinction coefficient retrieved from the spaceborne lidar CALIOP(cloud-aerosol lidar with orthogonal polarization) showed that the springtime peak AOD could be attributed to an abrupt increase in aerosol loading between altitudes of 2 and 5 km.In contrast, aerosol loading in the low atmosphere(below 1 km) was only half of that in winter. Wind fields in the low and high atmosphere exhibited opposite transportation patterns in spring over the Gulf of Tonkin, implying different sources for each level. By comparing the emission inventory of anthropogenic sources with biomass burning, and analyzing the seasonal variation of the vertical structure of aerosols over the Northern Indo-China Peninsula(NIC), it was concluded that biomass burning emissions contributed to high aerosol loading in spring. The relatively high topography and the high surface temperature in spring made planetary boundary layer height greater than 3 km over NIC. In addition, small-scale cumulus convection frequently occurred, facilitating pollutant rising to over 3 km, which was a height favoring long-range transport. Thus, pollutants emitted from biomass burning over NIC in spring were raised to the high atmosphere, then experienced long-range transport, leading to the increase in aerosol loading at high altitudes over the Gulf of Tonkin during spring. | Xiaoli Shan Jun Xu Yixue Li Feng Han Xiaohui Du Jingying Mao Yunbo Chen Youjiang He Fan Meng Xuezhi Dai | 2016 | Journal of Environmental Sciences2016，28，2： | 2 |
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