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| 1 | MIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes显示文摘piRNA 机械在调停以它的角色著名 transposons 的 epigenetic silencing。最近的研究建议这功能也包含导出 transposon 的抄本的指导 piRNA 的劈开。同样多 piRNAs 也看起来有能力指向多样的 mRNAs,这提起 piRNAs 可以与 siRNAs 比广泛地扮演降级的吸引人的可能性特定的 mRNAs。直接测试这个假设,我们比较了联系的老鼠 PIWI (MIWI ) 有从老鼠睾丸的试验性地识别的劈开的 mRNA 碎片的 piRNAs,和主要发生在的观察劈开地点从 5 ′ 放 10;通常认为的指向结束 piRNAs。我们也注意了强壮的偏爱因为分别地,在核苷酸的 U 和 A 残余在 piRNAs 和 mRNA 碎片放 1 和 10,由“乒乓球”类似于 piRNA 扩大的模式的特征骑车。通过由介绍的 CLIP-seq 和基因表示 MIWI-RNA 相互作用印射,我们发现许多潜在的指向 piRNA 的 mRNAs 直接与 MIWI 交往,表演在 Miwi 的睾丸提高了表达式层次催化变异的鼠标。基于记者的试金进一步揭示了在调停 piRNA 的目标压抑的为 slicer 活动和 MIWI 的装载 piRNA 能力的在 piRNAs 和 mRNA 目标和要求之间的基础配对的重要性。重要地,我们证明某些关键 piRNA 目标的那合适的周转为精子形成是必要的。一起,这些调查结果为男细菌房间开发和成熟在鼠标睾丸和它的中央要求揭示 piRNA 机械的象 siRNA 一样函数。 | Peng Zhang Jun-Yan Kang Lan-Tao GOU Jiajia Wang Yuanchao Xue Geir Skogerboe Peng Dai Da-Wei Huang Runsheng Chen Xiang-Dong Fu Mo-Fang Liu Shunmin He | 2015 | Cell Research2015，25，2： | 35 |
| 2 | A Global Identification and Analysis of Small Nucleolar RNAs and Possible Intermediate-Sized Non-Coding RNAs in Oryza sativa显示文摘积累的证据建议非编码的 RNA (ncRNAs ) 在许多真核细胞的有机体普遍、机能上地重要。在这研究,我们采用了分别和 cDNA 图书馆构造方法列在后面由的一种特殊尺寸 454 系统地介绍米饭的深定序中间尺寸的 ncRNAs。我们的分析总共导致了 1349 ncRNAs 的鉴定,包括一个未知功能的范畴的 754 新奇 ncRNAs。所有识别 ncRNAs 的染色体分发没显示出海滨偏爱,并且显示了类似于与很少染色体相关性在编码蛋白质的基因观察了那的一个模式。非常, ncRNAs 的一半被集中在附近编码区域的 5 和 3 个终点正海滨。新奇 ncRNAs 的多数是米饭特定,当 78% 小核仁的 RNA (snoRNAs ) 被保存时。双人脚踏车复制驾驶了扩大在 snoRNA 基因家庭的一半上。而且, 90% snoRNA 候选人被显示特别地生产在 2030 nt,其 80% 通常与淘金者蛋白质被联系,和 AGO1b 之间的小 RNA。总的来说,我们的调查结果在 monocot 种提供中间尺寸的非编码的 transcriptome 的一个全面看法,它将为 ncRNA 函数的深入的分析用作一个有用平台。 | Ting-Ting Liu Danmeng Zhu Wei Chen Wei Deng Hang He Guangming He Baoyan Bai Yijun Qi Runsheng Chen Xing Wang Deng | 2013 | Molecular Plant2013，6，3： | 10 |
| 3 | Genomic Features and Regulatory Roles of Intermediate-Sized Non-Coding RNAs in Arabidopsis显示文摘在染色体宽的技术的最近的进展与各种各样的尺寸 ineukaryotes 允许几千非编码的 RNA 的鉴定,其中一些进一步被显示了在许多生物进程服务重要函数。然而在 modelplant Arabidopsis,新奇中介大小的 ncRNAs (im-ncRNAs )(50 ~ 300 nt ) 很限制了信息。由与深定序的技术使用修改隔离 strategycombined,我们全球性在 Arabidopsis 识别了 838 im-ncRNAs。多于一半(58%) 是新 ncRNA 种类,主要进化分叉。有趣地,与 5-UTR-derived 小说 im-ncRNAs 注解了 protein-codinggenes 趋于高度被表示。为 intergenic im-ncRNAs,他们比得上在幼苗的 mRNAs 的平均 abundanceswere,而是子集,在开始衰老的展出显著地更低的表示离开。进一步, intergenic im-ncRNAs 被调整由类似基因并且编码蛋白质的基因的到那些的 epigenetic 机制,和 someshowed 发展地调整了表示模式。基因屏蔽显示出的大规模颠倒 down-regulationof 很多 im-ncRNAs 在 vivo 导致了明显的分子的变化或反常发展显型,在植物生长和开发显示 im-ncRNAs 的功能的重要性。一起,我们的结果证明 thatnovel Arabidopsis im-ncRNAs 发展地被调整,功能的部件在 transcriptome.Key 词发现了: | Yuqiu Wang Xuncheng Wang Wei Deng Xiuduo Fan Ting-Ting Liu Guangming He Runsheng Chen William Terzaghi Danmeng Zhu Xing Wang Deng | 2014 | Molecular Plant2014，7，3： | 9 |
| 4 | Integrated transcriptomic and metabolomic analyses of a wax deficient citrus mutant exhibiting jasmonic acid-mediated defense against fungal pathogens显示文摘Naturally,resistant crop germplasms are important resources for managing the issues of agricultural product safety and environment deterioration.We found a spontaneous mutant of‘Newhall’navel orange(Citrus sinensis Osbeck)(MT)with broad-spectrum protections against fungal pathogens in the orchard,postharvest-storage,and artificial inoculation conditions.To understand the defense mechanism of MT fruit,we constructed a genome-scale metabolic network that integrated metabolome and transcriptome datasets.The coordinated transcriptomic and metabolic data were enriched in two sub-networks,showing the decrease in very long chain fatty acid(by 41.53%)and cuticular wax synthesis(by 81.34%),and increase in the synthesis of jasmonic acid(JA)(by 95.23%)and JA-induced metabolites such as 5-dimethylnobietin(by 28.37%)in MT.Furthermore,cytological and biochemical analyses confirmed that the response to fungal infection in MT was independent of wax deficiency and was correlated with the levels of jasmonates,and the expression of plant defensin gene PDF1.2.Results of exogenous application of MeJA and JA inhibitors such as propyl gallate proved that JA-mediated defense contributes to the strong tolerance against pathogens in MT.Our results indicated that jasmonate biosynthesis and signaling are stimulated by the fatty acid redirection of MT,and participate in the tolerance of pathogenic fungi. | Yizhong He Jingwen Han Runsheng Liu Yuduan Ding Jinqiu Wang Li Sun Xiaoming Yang Yunliu Zeng Weiwei Wen Juan Xu Hongming Zhang Xiang Yan Zhaoxing Chen Zuliang Gu Hong Chen Huanqing Tang Xiuxin Deng Yunjiang Cheng | 2018 | Horticulture Research2018，5，1： | 8 |
| 5 | Noncoding RNA:from dark matter to bright star显示文摘The central dogma states that genes encoded in the DNA should be first transcribed into messenger RNA(mRNA)and then translated into functional proteins(Crick,1970).This dogma has been written in numerous textbooks and learned by myriad students.However,along with the completion of the human genome project in June 2000,an astonishing fact was revealed:only 1.5%of the human genome encodes for proteins(Lander et al.,2001;Venter et al.,2001).This fact raised three fundamental questions:(i)why does the human genome have so few protein-coding genes?(ii)how to explain the apparent differences between humans and other species using the limited coding genes?(iii)what are the roles of the noncoding regions in our genome? | Yuanchao Xue Runsheng Chen Lianghu Qu Xiaofeng Cao | 2020 | Science China(Life Sciences)2020，63，4： | 6 |
| 6 | 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 |
| 7 | TDP-43 regulates cancer-associated microRNAs显示文摘 | Xiaowei Chen Zhen Fan Warren McGee Mengmeng Chen Ruirui Kong Pushuai Wen Tengfei Xiao Xiaomin Chen Jianghong Liu Li Zhu Runsheng Chen Jane Y. Wu | 2018 | Protein & Cell2018，9，10： | 4 |
| 8 | Identification of selenocyst-eine insertion sequence(SECIS) element in eukaryotic selenoproteins by RNA Draw program显示文摘The computer program RNA Draw was used to identify the secondary structures in the 3’untranslated regions (3’UTRs) of the mRNAs from 46 eukaryotic seleno-proteins among 7 species. The program found one or two possible SECIS elements in these selenoproteins. The SECIS element consists of a stem-loop or hairpin structure with three conserved sequences of AUGA-(A)AA-GA. SECIS element was not found by the RNA Draw program in randomly selected non-selenoproteins. The results showed that SECIS element is the unique character of the genes ofeukaryotic selenoproteins. Thus it is possible to use RNA Draw to search the SECIS elements in gene bank for potential new selenoproteins. | XU Huibi HUANG Kaixun QU Xianghu GAO Zhonghong LIU Qiong CHEN Runsheng XUAN Zhenyu | 2001 | Chinese Science Bulletin2001，46，14： | 2 |
| 9 | Light-induced protein translocation by genetically encoded unnatural amino acid in Caenorhabditis elegans显示文摘Dear Editor,Living systems such as Caenorhabditis elegans are organized by interaction networks of biopolymer and small mol-ecules.The molecular engineering of specifi c targets to monitor and control these biological molecules has led to significant advances in our understand-ing of how biological systems are organ-ized,maintain themselves and disin-tegrate(Prescher and Bertozzi,2005).For instance,green fl uorescent protein(GFP)derived from jellyfi sh Aequorea Victoria helps us to accurately locate and observe proteins over long term periods.In addition,many novel LOV(light,oxy-gen,or voltage)domains such as LOV2-Jαand Vivid offer the possibility of cell-based motility management and tissue-based gene expression control(Wu et al.,2009;Wang et al.,2012). | Hao Chang Mei Han Wenming Huang Guifeng Wei Juanjuan Chen Peng R.Chen Runsheng Chen Junlong Zhang Tao Xu Pingyong Xu | 2013 | Protein & Cell2013，4，12： | 2 |
| 10 | Cep57, a NEDDl-binding pericentriolar material component, is essential for spindle pole integrity显示文摘 | Qixi Wu Runsheng He Haining Zhou Albert CH Yu Bo Zhang Junlin Teng Jianguo Chen | 2012 | Cell Research2012，22，9： | 2 |
| 11 | n-Octadecanethiol Self-Assembled Monolayer Coating with Microscopic Roughness for Dropwise Condensation of Steam显示文摘Here we presented a novel technology to achieve a Super-hydrophobic coating with microscopic roughness oncopper surface. First, make a layer of verdigris grow on the fresh pure copper surface. Gain it by exposing thecopper to air and the mist of acetic acid solution. The green coating is a mixture of basic copper(Ⅱ) carbonate andcopper(Ⅱ) acetate. Second heat the coating and make it decompose to CuO. Lastly, form an n-octadecanethiolself-assembled monolayers coating on the outermost surface. Contact angle test, scanning electron microscopeanalysis and electrochemical testing were carried out to characterize the surface, and a heat transfer experimentfor dropwise condensation of steam was performed also. Results show that the modified surface bears a few Super-hydrophobicfeatures, the static contact angle is higher than that in literatures, reaching 153.1±1.7°. The microscopicroughness can be seen in SEM images, differing much from H2O2 etched surface and bare copper surface.The condensation of steam on the surface is a typical form of dropwise condensation, in the measured rangeof temperature difference, under 0.1 MPa, the average convection heat transfer coefficients of the vertical surfaceare 1.7~2.1 times for those of film condensation. At the same time, the inhibition efficiency of surface is improvedto some extent comparing with the same kind of SAMs, which suggests that the lifetime of maintenancedropwise condensation would have the possibility to surpass the existing record. | Liang CHEN Shiqiang LIANG Runsheng YAN Yanjun CHENG Xiulan HUA Shuling CHEN | 2009 | Journal of Thermal Science2009，18，2： | 2 |
| 12 | Adaptive Binary Tree for Fast SVM Multiclass Classification 显示文摘 | Chen Jin Wang Cheng Wang Runsheng | 2009 | Neurocomputing2009，72，： | 1 |
| 13 | AlphaFold2 and its applications in the fields of biology and medicine显示文摘AlphaFold2(AF2)is an artificial intelligence(AI)system developed by DeepMind that can predict three-dimensional(3D)structures of proteins from amino acid sequences with atomic-level accuracy.Protein structure prediction is one of the most challenging problems in computational biology and chemistry,and has puzzled scientists for 50 years.The advent of AF2 presents an unprecedented progress in protein structure prediction and has attracted much attention.Subsequent release of structures of more than 200 million proteins predicted by AF2 further aroused great enthusiasm in the science community,especially in the fields of biology and medicine.AF2 is thought to have a significant impact on structural biology and research areas that need protein structure information,such as drug discovery,protein design,prediction of protein function,et al.Though the time is not long since AF2 was developed,there are already quite a few application studies of AF2 in the fields of biology and medicine,with many of them having preliminarily proved the potential of AF2.To better understand AF2 and promote its applications,we will in this article summarize the principle and system architecture of AF2 as well as the recipe of its success,and particularly focus on reviewing its applications in the fields of biology and medicine.Limitations of current AF2 prediction will also be discussed. | Zhenyu Yang Xiaoxi Zeng Yi Zhao Runsheng Chen | 2023 | Signal Transduction and Targeted Therapy2023，8，4： | 1 |
| 14 | SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling显示文摘Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames(s ORFs),which were usually missed in previous genome annotation.The significance of small proteins has been revealed in current years,along with the discovery of their diverse functions.However,systematic annotation of small proteins is still insufficient.Sm Prot was specially developed to provide valuable information on small proteins for scientific community.Here we present the update of Sm Prot,which emphasizes reliability of translated s ORFs,genetic variants in translated s ORFs,disease-specific s ORF translation events or sequences,and remarkably increased data volume.More components such as non-ATG translation initiation,function,and new sources are also included.Sm Prot incorporated638,958 unique small proteins curated from 3,165,229 primary records,which were computationally predicted from 419 ribosome profiling(Ribo-seq)datasets or collected from literature and other sources from 370 cell lines or tissues in 8 species(Homo sapiens,Mus musculus,Rattus norvegicus,Drosophila melanogaster,Danio rerio,Saccharomyces cerevisiae,Caenorhabditis elegans,and Escherichia coli).In addition,small protein families identified from human microbiomes were also collected.All datasets in Sm Prot are free to access,and available for browse,search,and bulk downloads at http://gffzz47cba05b3f0c4ad7hfc00wkxfb5cu6uff.ffgz.tsg.suse.edu.cn/SmProt/. | Yanyan Li Honghong Zhou Xiaomin Chen Yu Zheng Quan Kang Di Hao Lili Zhang Tingrui Song Huaxia Luo Yajing Hao Runsheng Chen Peng Zhang Shunmin He | 2021 | Genomics, Proteomics & Bioinformatics2021，19，4： | 1 |
| 15 | Fluid Evolution and Scheelite Precipitation Mechanism of the Large-Scale Shangfang Quartz-Vein-Type Tungsten Deposit, South China: Constraints from Rare Earth Element(REE) Behaviour during Fluid/Rock Interaction显示文摘Unlike classic skarn-type scheelite deposits directly acquiring sufficient Ca2+ from surrounding limestones, all of the scheelite orebodies of the Shangfang tungsten(W) deposit occur mainly in amphibolite, and this provides a new perspective on the mineralization mechanism of W deposits. The ability of hydrothermal scheelite(CaWO4) to bind REE3+ in their Ca2+ crystal lattices makes it a useful mineral for tracing fluid-rock interactions in hydrothermal mineralization systems. In this study, the REE compositions of scheelite and some silicate minerals were measured systematically in-situ by laser ablation inductively coupled plasma mass spectrometry(LA-ICP-MS) to assess the extent of fluid-rock interactions for the Late Mesozoic quartz-vein-type Shangfang W deposits. According to the variations in CaO and REE among scheelite and silicate minerals, the amphibole and actinolite in amphibolite may be able to release large amounts of Ca2+ and REE3+ into the ore-forming fluids during chlorite alteration, which is critical for scheelite precipitation. Furthermore, an improved batch crystallization model was adopted for simulating the process of scheelite precipitation and fluid evolution. The results of both the in-situ measurements and model calculations demonstrate that the precipitation of early-stage scheelite with medium rare-earth elements(MREE)-rich and [Eu/Eu*]N<1. The early-stage scheelite would consume more MREE than LREE and HREE of fluid, which will gradually produce residual fluids with strong MREE-depletion and [Eu/Eu*]N>1. Even though the partition coefficient of REE is constant, the later-stage scheelite will also inherit a certain degree of MREE-depletion and [Eu/Eu*]N future from the residual fluids. As a common mineral, sheelite forms in various types of hydrothermal ore deposits(e.g., tungsten and gold deposits). Hence, the improved batch crystallization model is also possible for obtaining detailed information regarding fluid evolution for other types of hydrothermal deposits. The results from model calculations also illustrate that the Eu anomalies of scheelite are not an effective index correlated to oxygen fugacity of fluids but rather are dominantly controlled by the continuous precipitation of scheelite. | Runsheng Chen Luyun Zhu Shao-Yong Jiang Ying Ma Qinghai Hu | 2020 | Journal of Earth Science2020，31，4： | 1 |
| 16 | CloudLCA: finding the lowest common ancestor in metagenome analysis using cloud computing显示文摘Estimating taxonomic content constitutes a key problem in metagenomic sequencing data analysis.However,extracting such content from high-throughput data of next-generation sequencing is very time-consuming with the currently available software.Here,we present CloudLCA,a parallel LCA algorithm that significantly improves the efficiency of determining taxonomic composition in metagenomic data analysis.Results show that CloudLCA(1)has a running time nearly linear with the increase of dataset magnitude,(2)displays linear speedup as the number of processors grows,especially for large datasets,and(3)reaches a speed of nearly 215 million reads each minute on a cluster with ten thin nodes.In comparison with MEGAN,a well-known metagenome analyzer,the speed of CloudLCA is up to 5 more times faster,and its peak memory usage is approximately 18.5%that of MEGAN,running on a fat node.CloudLCA can be run on one multiprocessor node or a cluster.It is expected to be part of MEGAN to accelerate analyzing reads,with the same output generated as MEGAN,which can be import into MEGAN in a direct way to finish the following analysis.Moreover,CloudLCA is a universal solution for finding the lowest common ancestor,and it can be applied in other fields requiring an LCA algorithm. | Guoguang Zhao Dechao Bu Changning Liu Jing Li Jian Yang Zhiyong Liu Yi Zhao Runsheng Chen | 2012 | Protein & Cell2012，3，2： | 1 |
| 17 | Evolutionarily Conserved Multisubunit RBL2/p130 and E2F4 Protein Complex Represses Human Cell Cycle-Dependent Genes in Quiescence显示文摘 | Larisa Litovchick Subhashini Sadasivam Laurence Florens Xiaopeng Zhu Selene K. Swanson Soundarapandian Velmurugan Runsheng Chen Michael P. Washburn X. Shirley Liu James A. DeCaprio | 2007 | Molecular Cell2007，，4： | 1 |
| 18 | Comparative analysis of surface wax in mature fruits between Satsuma mandarin ( Citrus unshiu ) and ‘Newhall’ navel orange ( Citrus sinensis ) from the perspective of crystal morphology, chemical composition and key gene expression显示文摘 | Jinqiu Wang Haohao Hao Runsheng Liu Qiaoli Ma Juan Xu Feng Chen Yunjiang Cheng Xiuxin Deng | 2013 | Food Chemistry2013，，： | 1 |
| 19 | Extracting contour lines from common-conditioned topographic maps显示文摘 | Chen Yang Wang Runsheng Qian Jing | 2006 | IEEE Transactions on Geosciences and Remote Sensing2006，44，4： | 1 |
| 20 | Adaptive binary tree for fast SVM muhiclass classification显示文摘 | Chen Jin Wang Cheng Wang Runsheng | 2009 | Neurocomput- ing2009，72，131415： | 1 |
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