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Reconstruction of the most recent common ancestor sequences of SARS-Cov S gene and detection of adaptive evolution in the spike protein

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Chinese Science Bulletin 2004年第12期49卷 1311-1313页

作者： ZHANG Yuan1, ZHENG Nan2,3, HAO Pei4,5.& ZHONG Yang6 1. Laboratory of Systematic and Evolutionary Botany, Institute of Bot- any, Chinese Academy of Sciences, Beijing 100093, china 2. College of Life Sciences, Beijing Normal University, Beijing 100875. china 3. Institute of Viral Disease Control and Prevention, Chinese CDC, Beijing 10005., china 4. bioinformation center, {5. Institutes for Biological Sciences, Chinese Academy of Sciences, {5. 200031, china 5. {5. center for bioinformation technology, shanghai 2.02.5, china 6. School of Life Sciences, Fudan University, {5. 200433, china 1. Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences 100093 Beijing China 2. College of Life Sciences Beijing Normal University 100875 Beijing China 3. Institute of Viral Disease Control and Prevention Chinese CDC 100052 Beijing China 4. bioinformation center Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 200031 Shanghai China 5. shanghai center for bioinformation technology 200235 Shanghai China 6. School of Life Sciences Fudan University 200433 Shanghai China

The genome oiganization and expression strategy of severe acute respiratory syndrome coronavirus (SARS-CoV) have been described extensively. As a structural glycoprotein on the virion surface, the spike protein is responsible for binding to host cellular receptors and for the fusion between the viral envelope and the cellular membrane. It also induces neutralizing antibodies in the host and mediates cellular immunity. Previous studies suggested that amino acid replacements in the spike protein coulddramatically alter the pathogenesis and virulence of some coronaviruses. It is therefore reasonable to test the hypothesis that radical amino acid replacements in the spike protein, favored by environmental selective pressure during the process of SARS-CoV interspecific transmission, might make this pathogen adapt to a new host, In this study, we investigated a total of 108 complete sequences of the SARS-CoV S gene from Gen-Bank (until March 23, 2004). After omission of those records containing frame-shift mutations or low quality sequences, e.g. ZJ01, and selection of one sequence for identical records, an alignment of 42 sequences was obtained using the program Clustal-X. Then, we reconstructed the most recent common ancestor (MRCA) sequences of theSARS-CoV S gene and detected the adaptive evolution in the spike protein.

关键词： SARS冠状病毒自适应进化基因表达糖蛋白分子免疫学波峰病毒

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Semantic Search among Heterogeneous Biological Databases Based on Gene Ontology

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Acta Biochimica et Biophysica Sinica 2004年第5期36卷 365-370页

作者： Shun-Liang CAO, Lei QIN1, Wei-Zhong HE1, Yang ZHONG2, Yang-Yong ZHU, and Yi-Xue LI1,3* Department of Computing and Information technology, Fudan University, shanghai 200433, china shanghai center for {5. 1 technology, shanghai 2.02.5, china School of Life Sciences, Fudan University, shanghai 200433, china {5. center of shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, shanghai 200031, china Department of Computing and Information technology Fudan University Shanghai China

Semantic search is a key issue in integration of heterogeneous biological databases. In this paper, we present a methodology for implementing semantic search in BioDW, an integrated biological data warehouse. Two tables are presented: the DB2GO table to correlate Gene Ontology (GO) annotated entries from BioDW data sources with GO, and the semantic similarity table to record similarity scores derived from any pair of GO terms. Based on the two tables, multifarious ways for semantic search are provided and the corresponding entries in heterogeneous biological databases in semantic terms can be expediently searched.

关键词： Gene Ontology semantic search BioDW

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Biological networks to the analysis of microarray data

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Progress in Natural Science:Materials International 2006年第12期16卷 1242-1251页

作者： FANG Zhuo~1, LUO Qingming~1**, ZHANG Guoqing~1 and LI Yixue~2**(1. Hubei Bioinformatics and Molecular Imaging Key Laboratory,Huazhong University of Science and technology, Wuhan 430074, china 2. shanghai center for bioinformation and technology, shanghai 2.02.5, china) [a]Hubei Bioinformatics and Molecular Imaging Key Laboratory Huazhong University of Science and Technology Wuhan China [b]shanghai center for bioinformation and technology Shanghai China

Microarray technology, which permits rapid and large-scale screening for patterns of gene expressions, usually generates a large amount of data. How to mine the biological meanings under these data is one of the main challenges in bioinformatics. Compared to the pure mathematical techniques, those methods incorporated with some prior biological knowledge generally bring better interpretations. Recently, a new analysis, in which the knowledge of biological networks such as metabolic network and protein interaction network is introduced, is widely applied to microarray data analysis. The microarray data analysis based on biological networks contains two main research aspects: identification of active components in biological networks and assessment of gene sets significance. In this paper, we briefly review the progress of these two categories of analyses, especially some representative methods.

关键词： biological networks microarray data analysis subnetwork gene set.

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Functional analysis of schistosomes EF-hand domain-containing tegument proteins

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Chinese Science Bulletin 2007年第15期52卷 2100-2107页

作者： YU FuDong1,2,3,KANG Bin1,3,LI YuanYuan3,4 & LI YiXue1,3 1 Bioinformatics center,Key Laboratory of Systems Biology,shanghai Institutes for Biological Sciences,Chinese Academy of Sci-ences,shanghai 200031,china 2 Graduate University of Chinese Academy of Sciences,shanghai 200031,china 3 shanghai center for bioinformation technology,shanghai 2.02.5,china 4 Key Laboratory of Systems Biology,shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,shanghai 200031,china Bioinformatics center Key Laboratory of Systems Biology Shanghai Institutesfor Biological Sciences Chinese Academy of Sciences Shanghai 200031 China

Schistosomes cause schistosomiasis disease which severely threatens human health. Little is known about the functions of EF-hand domain containing schistosomes tegument proteins other than as an-tigens. More possible functions of these tegument proteins were investigated with in silico analyses including protein-protein functional interaction,site-specific variation and glycosylation modification. The analysis results suggested that schistosomes could actively modulate host immune responses for its own favor through functional interactions with host proteins with immunomodulatory function,and passively regulate host immune responses through sequence variation under positive selection and glycosylating the recognition sites of host immune attack. In addition,the analysis of the C-terminal domain of these tegument proteins indicated that they could assist schistosomes in escaping host immune attacks through inhibiting chemotaxis and non-complement fixing antibody (IgG4) responses. In summary,our results suggested that these tegument antigen proteins could assist schistosomes in escaping and modulating host immune responses for self-protection during the process of host-para-site interaction.

关键词：寄生虫血吸虫皮蛋白质健康

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Learn to fight from the war

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Chinese Science Bulletin 2009年第13期54卷 2157-2158页

作者： ZHAO GuoPing shanghai-MOST Key Laboratory for Disease and Health Genomics,Chinese National Human Genome center at shanghai,shanghai 201203,china Lab of Synthetic Biology,shanghai Institutes of Biological Sciences,Chinese Academy of Sciences,shanghai 200031,china National Engineering Research center for Biochip technology,shanghai Biochip Co.Ltd.,shanghai 201203,china School of Life Sciences,Fudan University,shanghai 200433,china ZHONG Yang School of Life Sciences,Fudan University,shanghai 200433,china shanghai center for bioinformation technology,shanghai 2.02.5,china shanghai-MOST Key Laboratory for Disease and Health Genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China Lab of Synthetic Biology Shanghai Institutes of Biological Sciences Chinese Academy of Sciences Shanghai 200031 China National Engineering Research center for Biochip technology Shanghai Biochip Co. Ltd. Shanghai 201203 China School of Life Sciences Fudan University Shanghai 200433 China shanghai center for bioinformation technology Shanghai 200235 China

In March 2009,a novel type A (H1N1) influenza broke out in North America and rapidly spread all over the world.

关键词：世界卫生组织战争军备竞赛 WHO 流感

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Association of DRD2 polymorphisms and chlorpromazine-induced extrapyramidal syndrome in Chinese schizophrenic patients

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Acta Pharmacologica Sinica 2006年第8期27卷 966-970页

作者： Sheng-nan WU~(2,3,5.6) Rui GAO~(2,3,6) Qing-he XING~(2,3,6) Hua-fang LI~4 Yi-feng SHEN~4 Niu-fan GU~4 Guo-yin FENG~4 Lin HE~(2,3,7)2 Bio-X Life Science Research center,shanghai Jiaotong University,shanghai 200030,china 3 Institute of Nutritional Sciences,SIBS,Chinese Academy of Sciences,shanghai 200031,china 4 shanghai Institute of Mental Health,shanghai 200030,china 5.shanghai Institute of Hypertension,Ruijin Hospital,Medical School of shanghai Jiaotong University,shanghai 200025.china Bio-X Life Science Research center Shanghai Jiaotong University Shanghai 200030 China

Aim:Extrapyramidal syndrome (EPS) is most commonly affected by typical antip-sychotic drugs that have a high affinity with the D2 ***,manyresearch groups have reported on the positive relationship between the geneticvariations in the DRD2 gene and the therapeutic response in schizophrenia pa-tients as a result of the role of variations in the receptor in modulating *** this study,we evaluate the role DRD2 plays in chlorpromazine-induced EPS in schizophrenic ***:We identified seven SNP(singlenucleotide polymorphism) (-141Cins>del,TaqIB,TaqID,Ser311Cys,rs6275.rs6277and TaqIA) in the DRD2 gene in 146 schizophrenic inpatients (5. with EPS and 87without EPS according to the Simpson-Angus Scale) treated with chlorpromazineafter 8 *** alleles of all loci were determined by PCR (polymerase chainreaction).Results:Polymorphisms TaqlD,Ser311Cys and rs6277 were not poly-morphic in the population recruited in the present *** statistical signifi-cance was found in the allele distribution of-141Cins>del,TaqIB,rs6275.andTaqIA or in the estimated haplotypes (constituted by TaqIB,rs6275.and TaqIA) inlinkage disequilibrium between the two ***:Our results did notlend strong support to the view that the genetic variation of the DRD2 gene playsa major role in the individually variable adverse effect induced by chlorpromazine,at least in Chinese patients with *** results confirmed a previousstudy on the relationship between DRD2 and EPS in Caucasians.

关键词： dopamine receptors basal ganglia disease polymorphism chlorpromazine schizophrenia

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EMMA:An Efficient Massive Mapping Algorithm Using Improved Approximate Mapping Filtering

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Acta Biochimica et Biophysica Sinica 2006年第12期38卷 857-864页

作者： Xin ZHANG~1 Zhi-Wei CAO~2 Zhi-Xin LIN~3 Qing-Kang WANG~1* Yi-Xue LI~4 1 Institute of Micro/Nano Science and technology,shanghai Jiaotong University,shanghai 200030,china 2 shanghai {5. for bioinformation technology,shanghai 2.02.5,china 3 College of Life Science and technology,shanghai Jiaotong University,shanghai 200030,china 4 bioinformation {5. of shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,shanghai 200031,china shanghai center for bioinformation technology Shanghai 200235China Institute of Micro/Nano Science and technology Shanghai Jiaotong UniversityShanghai 200030China

Efficient massive mapping algorithm (EMMA),an algorithm on efficiently mapping massivecDNAs onto genomic sequences,has recently been *** process of mapping massive cDNAsonto genomic sequences has been improved using more approximate mapping filtering based on an enhancedsuffix array coupled with a pruned fast hash table,algorithms of block alignment extensions,and *** compared with the classical BLAT software in this field,the computing of EMMA ranges fromtwo to forty-one times faster under similar prediction precisions.

关键词： cDNA mapping maximal exact match enhanced suffix array pruned fast hash table extension algorithm

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Protein Secondary Structure Prediction Using Dynamic Programming

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Acta Biochimica et Biophysica Sinica 2005年第3期37卷 167-172页

作者： Jing ZHAO Pei-Ming SONG Qing FANG Jian-Hua LUO School of Life Science & technology,shanghai Jiaotong University,shanghai 200240,china shanghai {5. for bioinformation and technology,shanghai 2.02.5,china Logistical Engineering University,Chongqing 400016,china School of Life Science & technology Shanghai Jiaotong University Shanghai 200240 China

In the present paper,we describe how a directed graph was constructed and then searched forthe optimum path using a dynamic programming approach,based on the secondary structure propensity ofthe protein short sequence derived from a training data *** protein secondary structure was thus pre-dicted in this *** average three-state accuracy of the algorithm used was 76.70%.

关键词： directed graph dynamic programming approach protein secondary structure

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The contribution of cis-regulatory elements to head-to-head gene pairs' co-expression pattern

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Science china(Life Sciences) 2009年第1期52卷 74-79页

作者： HAO Pei1,2,YU Yao2,3,ZHANG XiaoYan4,TU Kang2,FAN HaiWei2 & ZHONG Yang1 1 School of Life Sciences,Fudan University,shanghai 200433,china 2 Bioinformatics center,Key Lab of Systems Biology,shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,shanghai 200031,china 3 shanghai center for bioinformation technology,shanghai 2.02.5,china 4 School of Life Sciences,Tongji University,shanghai 200092,china 1. School of Life Sciences Fudan University Shanghai 200433 China 2. Bioinformatics center Key Lab of Systems Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China 3. shanghai center for bioinformation technology Shanghai 200235 China 4. School of Life Sciences Tongji University Shanghai 200092 China

Transcription regulation is one of the most critical pipelines in biological process,in which cis-elements play the role as gene expression *** attempt to deduce the principles underlying the co-expression of "head-to-head" gene pairs by analyzing activities or behaviors of the shared cis-elements.A network component analysis was performed to estimate the impact of cis-elements on gene promoters and their activities under different *** discoveries reveal how biological system uses those regulatory elements to control the expression pattern of "head-to-head" gene pairs and the whole transcription regulation system.

关键词： transcription regulation cis-elements "head-to-head" gene pairs

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Phylogeographic analysis of human papillomavirus 5.

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Science china(Life Sciences) 2009年第12期52卷 1164-1172页

作者： LI YanYun1, LI ZuoFeng2, HE YiFeng1, KANG Yu1, ZHANG XiaoYan1, CHENG MingJun1, ZHONG Yang2, 3· & XU CongJian1· 1 Obstetrics and Gynecology Hospital of Fudan University, shanghai 200011, china 2 shanghai bioinformation Research center,{5., china 3 School of Life Sciences, Fudan University, shanghai 200433, china Obstetrics and Gynecology Hospital of Fudan University Shanghai 200011 China shanghai Bio-information Research center Shanghai 200235 China School of Life Sciences Fudan University Shanghai 200433 China

Human papillomavirus 5. (HPV5.) is one type of HPV with high risk of causing cervical cancer. Unusually high prevalence of HPV5. has been reported in Asia, Africa and some other areas. However, due to the scattered distribution of global data, in addition to the lack of data of some HPV5. high-incidence nations and regions, like china's Mainland, a comprehensive analysis of the global geographical distribution of HPV5. remains blank so far. In this study, HPV5. from the human cervical cancer tissue was detected in china's Mainland, and 14 new HPV5.-E6/L1 gene sequences were obtained. Moreover, phylogeographic analysis has been conducted combining the HPV5. sequences that have been deposited in GenBank since 1985. The study result shows that the sequences detected from the shanghai, Jiangsu and Sichuan areas are homologous with those found in the past from Hong Kong and Xi'an, china, as well as Japan and other Southeast Asian areas. Furthermore, Western Africa is considered to be the "root" source of the HPV5. variant, while china's Mainland and Southeast Asia are "transit points" and the new sources of HPV5. after receiving the isolates from the "root" source; like HPV16 and HPV18, the HPV5. might also be one of the major HPV types associated with the development and spread of cervical cancer.

关键词： human papillomavirus 5. (HPV5.) cervical cancer phylogeography molecular evolution

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