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| 1 | A complete sequence and comparative analysis of a SARS-associated virus(Isolate BJ01)显示文摘The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-associated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development of diagnostics, prevention by future vaccination, and treatment by developing new drugs. We report the complete genome sequence and comparative analysis of an isolate (BJ01) of the coronavirus that has been recognized as a pathogen for SARS. The genome is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA polymerase (composed of 2 ORFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses. The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative substitutions have been identified by comparative analysis of the 5 SARS- associated virus genome sequences in GenBank. Fifteen of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted alteration of physical and chemical features, have been detected in the S protein that is postulated to beinvolved in the immunoreactions between the virus and its host. Two amino acid changes have been detected in the Mprotein, which could be related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated viruses but provides noevidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated virus and ruling out conclusively the existence of otherpossible SARS-related pathogen(s). | QIN E'de ZHU Qingyu YU Man FAN Baochang CHANG Guohui SI Bingyin YANG Bao PENG Wenming JIANG Tao LIU Bohua DENG Yongqiang LIU Hong ZHANG Yu WANG Cui LI Yuquan GAN Yonghua LI Xiaoyu L Fushuang TAN Gang CAO Wuchun, YANG Ruifu Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China WANG Jian, LI Wei, XU Zuyuan, LI Yan, WU Qingfa, LIN Wei, CHEN Weijun, TANG Lin, DENG Yajun, HAN Yujun, LI Changfeng, LEI Meng, LI Guoqing, LI Wenjie, L Hong, SHI Jianping, TONG Zongzhong, ZHANG Feng, LI Songgang, LIU Bin, LIU Siqi, DONG Wei, WANG Jun, Gane K-S Wong, YU Jun & YANG Huanming* Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300 National Center for Genome Information, Beijing 101300, China | 2003 | Chinese Science Bulletin2003，48，10： | 121 |
| 2 | Glutamine synthetase as an early marker for hepatocellular carcinoma based on proteomic analysis of resected smal hepatocel ular carcinomas显示文摘BACKGROUND:Hepatocellular carcinoma(HCC)is a highly malignant tumor with a poor prognosis.Because small HCCs possess most of the characteristics of early HCC,we investigated small HCCs to screen potential biomarkers for early diagnosis.METHODS:Proteins were extracted from 10 sets of paired tissue samples from HBV-infected small-HCC patients.The extracted proteins were well resolved by two-dimensional electrophoresis.These HCC-associated proteins were then identified by MALDI-TOF/TOF MS following image analysis.Western blotting and immunohistochemistry were used to assess glutamine synthetase(GS)and phenazine biosynthesislike domain-containing protein(PBLD)expression in liver tissue.Enzyme-linked immunosorbent assays in 152 serum samples(from 49 healthy donors,24 patients with liver cirrhosis,and 79 with HCC)were used to further assess the significance of GS clinically.RESULTS:Fifteen up-regulated and three down-regulated proteins were identified.Western blotting confirmed GS overexpression and decreased PBLD expression in liver tissue.Immunohistochemistry showed that GS was expressed in 70.0%(84/120)of HCCs and 35.8%(43/120)of nontumor tissues;PBLD was expressed in 74.2%(89/120) of nontumor tissues and 40.8%(49/120)of HCCs.The Chi-square test showed significant expression differences between HCCs and adjacent tissues.Consistent with this,serum GS levels in HCC patients were significantly higher than those in liver cirrhosis patients and healthy donors,while the latter two groups were also significantly different.In addition, a diagnostic cutoff value of 2.6 mg/ml was used for GS;it was elevated in 19(76.0%)of 25 HCC patients with AFP≤20 ng/ml and 47(88.7%)of 53 HCC patients with AFP≤200 ng/ml.CONCLUSION:GS and PBLD are abnormally expressed in most HCCs.GS may be a novel serum marker for early HCC, especially for those patients with low AFP levels(≤200 ng/ml). | Jiang Long,Zhen-Wei Lang,Hua-Guang Wang,Tai-Ling Wang,Bao-En Wang and Si-Qi Liu Liver Research Center,Beijing Friendship Hospital, Capital Medical University,Beijing 100050,China Department of Hepatology,Department of Pathology, Beijing Youan Hospital,Capital Medical University,Beijing 100069,China Department of Pharmaceutical Affairs,Beijing Chaoyang Hospital,Capital Medical University,Beijing 100020,China Department of Pathology,China-Japan Friendship Hospital,Beijing 100029,China Beijing Genomics Institute,Chinese Academy of Science,Beijing Airport Industrial Zone B-6,Shunyi,Beijing 101300,China | 2010 | Hepatobiliary & Pancreatic Diseases International2010，9，3： | 21 |
| 3 | The Epitope Study on the SARS-CoV Nucleocapsid Protein显示文摘The nucleocapsid protein (N protein) has been found to be an antigenic protein in a number of coronaviruses. Whether the N protein in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is antigenic remains to be elucidated. Using Western blot and Enzyme-linked Immunosorbent Assay (ELISA),the recombinant N proteins and the synthesized peptides derived from the N protein were screened in sera from SARS patients. All patient sera in this study displayed strong positive immunoreactivities against the recombinant N proteins,whereas normal sera gave negative immunoresponses to these proteins, indicating that the N protein of SARS-CoV is an antigenic protein. Furthermore, the epitope sites in the N protein were determined by competition experiments, in which the recombinant proteins or the synthesized peptides competed against the SARS-CoV proteins to bind to the antibodies raised in SARS sera. One epitope site located at the C-terminus was confirmed as the most antigenic region in this protein. A detailed screening of peptide with ELISA demonstrated that the amino sequence from Codons 371 to 407 was the epitope site at the C-terminus of the N protein. Understanding of the epitope sites could be very significant for developing an effective diagnostic approach to SARS. | Shuting Li, Liang Lin, Hao Wang, Jianning Yin, Yan Ren, Zhe Zhao, Jie Wen, Cuiqi Zhou, Xumin Zhang, Xiaolei Li, Jingqiang Wang, Zhengfeng Zhou, Jinxiu Liu, Jianmin Shao, Tingting Lei, Jianqiu Fang, Ningzhi Xu, and Siqi LiuBeijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China & Beijing Proteomics Institute, Beijing 101300, China | 2003 | Genomics, Proteomics & Bioinformatics2003，1，3： | 9 |
| 4 | Evaluation of Six Methods for Estimating Synonymous and Non-synonymous Substitution Rates显示文摘Methods for estimating synonymous and nonsynonymous substitution rates among protein-coding sequences adopt different mutation (substitution) models with sub- tle yet significant differences, which lead to different estimates of evolutionary information. Little attention has been devoted to the comparison of methods for obtaining reliable estimates since the amount of sequence variations within tar- geted datasets is always unpredictable. To our knowledge, there is little informa- tion available in literature about evaluation of these different methods. In this study, we compared six widely used methods and provided with evaluation results using simulated sequences. The results indicate that incorporating sequence fea- tures (such as transition/transversion bias and nucleotide/codon frequency bias) into methods could yield better performance. We recommend that conclusions related to or derived from Ka and Ks analyses should not be readily drawn only according to results from one method. | Zhang Zhang1,2,3 and Jun Yu1,2,4* 1 Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China 2 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China 3Graduate School, Chinese Academy of Sciences, Beijing 100039, China 4James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310007, China. | 2006 | Genomics, Proteomics & Bioinformatics2006，4，3： | 7 |
| 5 | DNA barcoding provides distinction between Radix Astragali and its adulterants显示文摘Based on variable nuclear and/or organellar DNA sequences among vastly divergent species as well as morphologically indistinguishable species, DNA barcoding is widely applicable in species identification, biodiversity studies, forensic analyses, and authentication of medicinal plants. The roots of Astragalus membranaceus and A. membranaceus var. mongholica are commonly used as Radix Astragali in several Asian countries, including China, Japan, and Korea. However, in addition to the two species recorded in the Chinese Pharmacopoeia, there are twenty-three species from different genera including Astragalus, Oxytropis, Hedysarum, and Glycyrrhiza, which have been used as adulterants not only in trading markets but also by the herbal medicine industry. Therefore, a simple, reliable, and accurate classification method is important for distinguishing authentic Radix Astragali from its adulterants. In this study, we acquired data for 37 samples from four related genera within the family Fabaceae. Then we compared four candidate DNA barcoding markers using ITS, matK, rbcL, and coxI sequences from nuclear, chloroplast, and mitochondrial genomes, all commonly used for plants to identify genetic variations among genera, intraspecies, and interspecies. We observed higher divergences among genera and interspecies for ITS, which have the average Kimura 2-parameter distances of 4.5% and 14.1%, respectively, whereas matK was found to have sufficient divergence at the intraspecific level. Moreover, two indels detected in the matK sequence are useful for PCR studies in distinguishing Radix Astragali from its adulterants. This study suggests that the combined barcoding regions of ITS and matK are superior barcodes for Radix Astragali and further studies should focus on evaluating the applicability and accuracy of such combined markers for a wide range of traditional Chinese herbs. | GUO HaiYan1,2, WANG WeiWei2, YANG Ning2, GUO BaoLin3, ZHANG Sun2, YANG RuiJing2, YUAN Ye2, YU JunLin4, HU SongNian2, SUN QiShi1 & YU Jun2 1School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China 2Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China 3Chinese Academy of Medical Sciences, Peking Union Medical College Institute of Medicinal Plant Development, Beijing 100094, China 4Department of Chemistry, Tonghua Normal College, Tonghua 134002, China | 2010 | Science China(Life Sciences)2010，53，8： | 7 |
| 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 | Prokaryote phylogeny meets taxonomy: An exhaustive comparison of composition vector trees with systematic bacteriology显示文摘We perform an exhaustive, taxon by taxon, comparison of the branchings in the composition vector trees (CVTrees) inferred from 432 prokaryotic genomes available on 31 December 2006, with the bacte-riologists' taxonomy-primarily the latest online Outline of the Bergey's Manual of Systematic Bacteri-ology. The CVTree phylogeny agrees very well with the Bergey's taxonomy in majority of fine branchings and overall structures. At the same time most of the differences between the trees and the Manual have been known to biologists to some extent and may hint at taxonomic revisions. Instead of demonstrating the overwhelming agreement this paper puts emphasis on the biological implications of the differences. | GAO Lei1,2, QI Ji1**, SUN JianDong2,3 & HAO BaiLin1,2,4 1 Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100080, China 2 T-Life Research Center, Fudan University, Shanghai 200433, China 3 Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 4 Santa Fe Institute, Santa Fe, NM87501, USA Center for Comparative Genomics and Bioinformatics, Penn State University, 310 Wartik Building, University Park, PA16802, USA | 2007 | Science China(Life Sciences)2007，50，5： | 4 |
| 8 | 水稻(籼稻)基因组工作框架图与精细图的绘制显示文摘2002年12月12日,中国科学院、国家科技部、国家计划委员会、国家自然科学基金委员会联合宣布“中国水稻(籼稻)基因组精细图完成”。此前,我国科学家于2001年10月完成了其工作框架图的绘制。水稻(籼稻)基因组工作框架图与精细图是继人类基因组计划之后所测定完成的最大的植物基因组,也是迄今为止惟一用“霰弹法”完成的最大基因组精细图。这表明中国在基因组科学领域处于世界领先地位;也标志着中国的高性能计算在生物信息领域的综合实力。文章概要地介绍了该项成果的研究背景和意义、主要内容、研制过程和方法、应用价值及国内外的评价。 | BGI,CAS,Beijing 101300) | 2003 | 中国科学院院刊2003，18，1： | 4 |
| 9 | Origin and evolution of new exons in the rodent zinc fingerprotein 39 gene显示文摘The origin of new structures and functions is an important process in evolution. In the past decades, we have obtained some preliminary knowledge of the origin and evo- lution of new genes. However, as the basic unit of genes, the origin and evolution of exons remain unclear. Because young exons retain the footprints of origination, they can be good materials for studying origin and evolution of new exons. In this paper, we report two young exons in a zinc finger protein gene of rodents. Since they are unique sequences in mouse and rat genome and no homologous sequences were found in the orthologous genes of human and pig, the young exons might originate after the divergence of primates and rodents through exonization of intronic sequences. Strong positive selection was detected in the new exons between mouse and rat, suggesting that these exons have undergone significant functional divergence after the separation of the two species. On the other hand, population genetics data of mouse dem- onstrate that the new exons have been subject to functional constraint, indicating an important function of the new exons in mouse. Functional analyses suggest that these new exons encode a nuclear localization signal peptide, which may me- diate new ways of nuclear protein transport. To our knowl- edge, this is the first example of the origin and evolution of young exons. | PENG Lixin1,2*, ZHENG Hongkun3*, LI Xin1,2, YANG Shuang2,4, CHEN Hong1,5 & WANG Wen2 1. College of Animal Science and Technology, Northwest Sci-Tech Uni- versity of Agriculture and Forestry, Yangling 712100, China 2. CAS-Max Planck Junior Scientist Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China 3. Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China 4. Graduate School of the Chinese Academy of Sciences, Beijing 100039 China 5. Institute of Cellular and Molecular Biology, Xuzhou Normal Univer- sity, Xuzhou 221116, China Correspondence should be addressed to Wang Wen (email: wwang@ mail.kiz.ac.cn) | 2005 | Chinese Science Bulletin2005，50，11： | 3 |
| 10 | Gene expression profiling in porcine mammary gland during lactation and identification of breed- and developmental-stage-specific genes显示文摘A total of 28941 ESTs were sequenced from five 5?-directed non-normalized cDNA li-braries, which were assembled into 2212 contigs and 5642 singlets using CAP3. These sequences were annotated and clustered into 6857 unique genes, 2072 of which having no functional annotations were considered as novel genes. These genes were further classified into Gene Ontology categories. By comparing the expression profiles, we identified some breed- and developmental-stage-specific gene groups. These genes may be relative to reproductive performance or play important roles in milk synthesis, secretion and mammary involution. The unknown EST sequences and expression profiles at different developmental stages and breeds are very important resources for further research. | SU Zhixi1, DONG Xinjiao2, ZHANG Bing1, ZENG Yanwu1, FU Yan1, YU Jun1,3 & HU Songnian1,3 1. James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China 2. School of Life and Environmental Sciences, Wenzhou Normal College, Wenzhou 325027, China 3. Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China | 2006 | Science China(Life Sciences)2006，49，1： | 3 |
| 11 | A Strategy for Searching Antigenic Regions in the SARS-CoV Spike Protein显示文摘In the face of the worldwide threat of severe acute respiratory syndrome (SARS)to human life, some of the most urgent challenges are to develop fast and accurate analytical methods for early diagnosis of this disease as well as to create a safe anti-viral vaccine for prevention. To these ends, we investigated the antigenicity of the spike protein (S protein), a major structural protein in the SARS-coronavirus (SARS-CoV). Based upon the theoretical analysis for hydrophobicity of the S protein, 18 peptides were synthesized. Using Enzyme-Linked Immunosorbent Assay (ELISA), these peptides were screened in the sera from SARS patients. According to these results, two fragments of the S gene were amplified by PCR and cloned into pET-32a. Both S fragments were expressed in the BL-21 strain and further purified with an affinity chromatography. These recombinant S fragments were confirmed to have positive cross-reactions with SARS sera, either by Western blot or by ELISA. Our results demonstrated that the potential epitope regions were located at Codons 469-882 in the S protein, and one epitope site was located at Codons 599-620. Identification of antigenic regions in the SARS-CoV S protein may be important for the functional studies of this virus or the development of clinical diagnosis. | Yan Ren, Zhengfeng Zhou, Jinxiu Liu, Liang Lin, Shuting Li, Hao Wang, Ji Xia, Zhe Zhao, Jie Wen, Cuiqi Zhou, Jingqiang Wang, Jianning Yin, Ningzhi Xu, and Siqi LiuBeijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China & Beijing Proteomics Institute, Beijing 101300, China. | 2003 | Genomics, Proteomics & Bioinformatics2003，1，3： | 1 |
| 12 | Science and Technology Is Not Simply Equal to Sci-Tech显示文摘The terms 'science' (Hanyu Pinyin: Kēxué) and'technology' (Jìshù), in western languages, are usu-ally used separately with different meanings or to-gether as 'science and technology'. However, theyare often mentioned as 'Kēxué Jìshù', or even abbre-viated as 'sci-tech (Kējì)' in China (It is used in asimilar way in Japan). | Xingmin LiGraduate School, Chinese Academy of Sciences, Beijing 100039, ChinaXin Zhang (Beijing Language and Culture University, Beijing 100083, China) and Wei Gong (Beijing Genomics Institute, Beijing 101300, China) | 2003 | Genomics, Proteomics & Bioinformatics2003，1，2： | 1 |
| 13 | Azolla-A Model Organism for Plant Genomic Studies显示文摘The aquatic ferns of the genus Azolla are nitrogen-fixing plants that have great potentials in agricultural production and environmental conservation. Azolla in many aspects is qualified to serve as a model organism for genomic studies because of its importance in agriculture, its unique position in plant evolution, its symbiotic relationship with the N2-fixing cyanobacterium, Anabaena azollae, and its moderate-sized genome. The goals of this genome project are not only to understand the biology of the Azolla genome to promote its applications in biological research and agriculture practice but also to gain critical insights about evolution of plant genomes. Together with the strategic and technical improvement as well as cost reduction of DNA sequencing, the deciphering of their genetic code is imminent. | Yin-Long Qiu, Jun Yu1 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA 2 Beijing Genomics Institute, Chinese Academy of Scicences, Beijing 101300, China 3 University of Washington Genome Center, Seattle, WA 98195, USA | 2003 | Genomics, Proteomics & Bioinformatics2003，1，1： | 1 |
| 14 | Being the Pioneer of Life Sciences in China——Introduction to Beijing Genomics Institute显示文摘The Beijing Genomics Institute (BGI) of Chinese Academy of Sciences (CAS) was officially founded in December 2003. Its predecessor, Beijing Huada Genomics Research Center, has presented significant contributions to the development of life sciences in China by its excellent scientific innovations and achievements in the last five years. | Xin Zhang Beijing Genomics Institute, Beijing 101300, China. | 2004 | Genomics, Proteomics & Bioinformatics2004，2，1： | 0 |
| 15 | DNA sequence comparative analysis of the 3pter-p26 region of human genome显示文摘Most proterminal regions of human chromosomes are GC-rich and gene-rich. Chromosome 3p is an exception. Its proterminal region is GC-poor, and likely to lose heterozygosity, thus causing a number of fatal diseases. Except one gap left in the telomeric position, the proterminal region of human chromosome 3p has been completely sequenced. The detailed sequence analysis showed: (i) the GC content of this region was 38.5%, being the lowest among all the human proterminal regions; (ii) this region contained 20 known genes and 22 predicted genes, with an average gene size of 97.5 kb. The previously mapped gene Cntn3 was not found in this region, but instead located in the 74 Mb position of human chromosome 3p; (iii) the interspersed repeats of this region were more active than the average level of the whole human genome, especially (TA)n, the content of which was twice the genome average; (iv) this region had a conserved synteny extending from 104.1 Mb to 112.4 Mb on the mouse chromosome 6, which was 8% larger in size, not in accordance with the whole genome comparison, probably because the 3pter-p26 region was more likely to lose neocleitides and its mouse synteny had more active interspersed repeats. | LUO Chunqing, LI Yan, ZHANG Xiaowei, ZHANG Yilin, ZHANG Haiqing, CHEN Chong, XU Zuyuan, CUI Peng, HU Songnian, YANG Huanming & DONG Wei Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China | 2005 | Science China(Life Sciences)2005，48，1： | 0 |
| 16 | Identification of new centrosome proteins by autoimmune patient sera显示文摘Compared to other subcellular organelles, centrosome proteome can hardly be studied, due to the dif- ficulties in separation and purification of centrosome. Auto-antisera from 6 autoimmune patients, which recognized centrosome specifically in immunofluorescence, were used to identify the corresponding centrosomal proteins. The sera were first tested by Western blot on whole cell lysate, and all bound antibodies were then eluted from each single band in Western blot membrane to assure which antibody was responsible for the centrosome specific immunofluorescence staining. The corresponding pro- teins were obtained by immunoprecipitation and identified by mass spectrometry. Six centrosomal proteins, including 2 known centrosomal proteins and 4 proteins with unknown localization or report- edly non-centrosomal localization, were identified. These proteins apparently involve in cell cycle regulation, signal transduction pathways, molecular chaperons, and metabolism enzymes, which may reflect the expected functional diversity of centrosome. | XIA Liang1, LI Yan1, YANG Dong1, WANG LiMin1, HE Fang1, ZHOU ChunYuan1, LI YongZhe2, ZENG ChangQing1 & He DaCheng1 1 Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, Beijing Normal University, Beijing 100875, China 2 Peking Union Medical Hospital, Peking Union Medical College, Beijing 100730, China 3 Beijing Genomic Institute, Beijing 101300, China | 2007 | Science China(Life Sciences)2007，50，2： | 0 |
| 17 | Applications of the double-barreled data in whole-genome shotgun sequence assembly and analysis显示文摘Double-barreled (DB) data have been widely used for the assembly of large ge- nomes. Based on the experience of building the whole-genome working draft of Oryza sativa L. ssp. Indica, we present here the prevailing and improved uses of DB data in the assembly pro- cedure and report on novel applications during the following data-mining processes such as ac- quiring precise insert fragment information of each clone across the genome, and a new kind of low-cost whole-genome microarray. With the increasing number of organisms being sequenced, we believe that DB data will play an important role both in other assembly procedures and in future genomic studies. | HAN Yujun 1,2 , NI Peixiang 2 , Lü Hong 2 , YE Jia 3 , HU Jianfei 1 , CHEN Chen 2 , HUANG Xiangang 2 , CONG Lijuan 2 , LI Guangyuan 2 , WANG Jing 1 , GU Xiaocheng 1 , YU Jun 2 & LI Songgang 1,2 1. College of Life Sciences, Peking University, Beijing 100871, China 2. Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3. James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310012, China | 2005 | Science China(Life Sciences)2005，48，3： | 0 |
| 18 | Comparative Analysis of Eubacterial DNA Polymerase III Alpha Subunits显示文摘DNA polymerase III is one of the five eubacterial DNA polymerases that is re-sponsible for the replication of DNA duplex. Among the ten subunits of the DNApolymerase III core enzyme, the alpha subunit catalyzes the reaction for polymer-izing both DNA strands. In this study, we extracted genomic sequences of thealpha subunit from 159 sequenced eubacterial genomes, and carried out sequence-based phylogenetic and structural analyses. We found that all eubacterial genomeshave one or more alpha subunits, which form either homodimers or heterodimers.Phylogenetic and domain structural analyses as well as copy number variations ofthe alpha subunit in each bacterium indicate the classification of alpha subunit intofour basic groups: polC, dnaE1, dnaE2, and dnaE3. This classification is of essencein genome composition analysis. We also consolidated the naming convention toavoid further confusion in gene annotations. | Xiao-Qian Zhao1,2,Jian-Fei Hu3,and Jun Yu1,4*1 Beijing Institute of Genomics,Chinese Academy of Sciences,Beijing 101300,China 2 Graduate School ofChinese Academy of Sciences,Beijing 100049,China 3College of Life Sciences,Peking University,Beijing100871,China 4James D.Watson Institute of Genome Sciences,Zhejiang University,Hangzhou 310008,China. | 2006 | Genomics, Proteomics & Bioinformatics2006，4，4： | 0 |
| 19 | A Novel Approach for Identifying the Heme-Binding Proteins from Mouse Tissues显示文摘Heme is a key cofactor in aerobic life, both in eukaryotes and prokaryotes. Because of the high reactivity of ferrous protoporphyrin IX, the reactions of heme in cells are often carried out through heme-protein complexes. Traditionally studies of hemebinding proteins have been approached on a case by case basis, thus there is a limited global view of the distribution of heme-binding proteins in different cells or tissues. The procedure described here is aimed at profiling hemne-binding proteins in mouse tissues sequentially by 1) purification of heme-binding proteins by hemeagarose, an affinity chromatographic resin; 2) isolation of heme-binding proteins by SDS-PAGE or two-dimensional electrophoresis; 3) identification of heme-binding proteins by mass spectrometry. In five mouse tissues, over 600 protein spots were visualized on 2DE gel stained by Commassie blue and 154 proteins were identified by MALDI-TOF, in which most proteins belong to heme related. This methodology makes it possible to globally characterize the heme-binding proteins in a biological system. | Xiaolei Li, Xiaoshan Wang, Kang Zhao, Zhengfeng Zhou, Caifeng Zhao, Ren Yan, Liang Lin, Tingting Lei, Jianning Yin, Rong Wang, Zhongsheng Sun, Znyuan Xu, Jingyue Bao, Xiuqing Zhang, Xiaoli Feng, and Siqi Liu* Beijing Genomics Institute, Chinese Academy of Sciences Beijing 101300, China | 2003 | Genomics, Proteomics & Bioinformatics2003，1，1： | 0 |
| 20 | Finding Signals for Plant Promoters显示文摘The strongest signal of plant promoter is searched with the model of single motif with two types.It turns out that the dominant type is the TATA-box.The other type may be called TATA-less signal,and may be used in gene finders for promoter recognition.While the TATA signals are very close for the monocot and the dicot,their TATA-less signals are significantly different.A general and flexible multi-motif model is also proposed for promoter analysis based on dynamic programming.By extending the Gibbs sampler to the dynamic programming and introducing temperature,an efficient algorithm is developed for searching signals in plant promoters. | Weimou ZhengInstitute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100080, China Beijing GenomicsInstitute, Chinese Academy of Sciences, Beijing 101300, China | 2003 | Genomics, Proteomics & Bioinformatics2003，1，1： | 0 |
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