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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 20024.,china shanghai Center for bioinformation and technology,shanghai 200235,china Logistical Engineering University,Chongqing 4.0016,china School of Life Science & technology Shanghai Jiaotong UniversityShanghai 200240 China shanghai Center for bioinformation and technologyshanghai 200235 China Logistical Engineering UniversityChongqing 4.0016 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

Recognition of Gene Acceptor Site Based on Multi-objective Optimization

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Acta Biochimica et Biophysica Sinica 2005年第7期37卷 435-439页

作者： Jing ZHAO~(1,3,4. Yue-Min ZHU~2 Pei-Ming SONG~1 Qing FANG~1 Jian-Hua LUO~(1,3) 1 School of Life Science & technology,shanghai Jiaotong University,shanghai 20024.,china 2 CREATIS,CNRS UMR 5515,INSA Lyon,69621 Villeurbanne Cedex,France 3 shanghai Center for bioinformation and technology,shanghai 200235,china 4.Logistical Engineering University,Chongqing 4.0016,china School of Life Science & technology Shanghai Jiaotong UniversityShanghai 200240 China shanghai Center for bioinformation and technologyshanghai 200235 China Logistical Engineering UniversityChongqing 4.0016 China CREATIS CNRS UMR 5515 INSA Lyon69621 Villeurbanne Cedex France

A new method for predicting the gene acceptor site based on multi-objective optimization isintroduced in this *** models for the acceptor,branch and distance between acceptor site andbranch site were constructed according to the characteristics of the sequences from the exon-intron databaseand using common biological *** acceptor function,branch function and distance functionwere defined respectively,and the multi-objective optimization model was constructed to recognize thesplice *** test results show that the algorithm used in this study performs better than the SplicePredictor,which is one of the leading acceptor site detectors.

关键词： multi-objective optimization acceptor site recognition

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 2004.3, china shanghai Center for {4. 1 technology, shanghai 200235, china School of Life Sciences, Fudan University, shanghai 2004.3, china {4. Center of shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, shanghai 200031, china Department of Computing and Information technology Fudan University Shanghai 200433 China shanghai Center for bioinformation technology shanghai 200235 China School of Life Sciences Fudan University Shanghai 200433 China bioinformation Center of shanghai Institutes for Biological Sciences the Chinese Academy of Sciences Shanghai 200031 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

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 200235,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 Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China Graduate University of Chinese Academy of Sciences Shanghai China shanghai Center for bioinformation technology Shanghai China Key Laboratory of Systems Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 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

Comparative Analysis of Two-component Signal Transduction System in Two Streptomycete Genomes

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Acta Biochimica et Biophysica Sinica 2007年第5期39卷 317-325页

Species of the genus Streptomyces are major bacteria responsible for producing most natural antibiotics. Streptomyces coelicolor A3(2) and Streptomyces avermitilis were sequenced in 2002 and 2003, respectively. Two-component signal transduction systems (TCSs), consisting of a histidine sensor kinase (SK) and a cognate response regulator (RR), form the most common mechanism of transmembrane signal transduction in prokaryotes. TCSs in S. coelicolor A3(2) have been analyzed in detail. Here, we identify and classify the SK and RR of S. avermitilis and compare the TCSs with those of S. coelicolor A3(2) by computational approaches. Phylogenetic analysis of the cognate SK-RR pairs of the two species indicated that the cognate SK-RR pairs fall into four classes according to the distribution of their orthologs in other organisms. In addition to the cognate SK-RR pairs, some potential partners of non-cognate SK-RR were found, including those of unpaired SK and orphan RR and the cross-talk between different components in either strain. Our study provides new clues for further exploration of the molecular regulation mechanism of streptomycetes with industrial importance.

关键词： Streptomyces two-component system cross-talk phylogenetic analysis

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 4.0074. china 2. shanghai Center for bioinformation and technology, shanghai 200235, china) Hubei Bioinformatics and Molecular Imaging Key Laboratory Huazhong University of Science and Technology Wuhan 430074 China shanghai Center for bioinformation and technology Shanghai 200235 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.

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 2004.3,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 School of Life Sciences Fudan University Shanghai China Bioinformatics Center Key Lab of Systems Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China shanghai Center for bioinformation technology Shanghai China School of Life Sciences Tongji University Shanghai 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

Anticoagulation property and security of artificial heart valve material

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Science china(Technological Sciences) 2005年第2期48卷 145-162页

作者： WANG Xianghui1, , LIU Xianghuai1,22, 3, ZHANG Feng2, LI Changrong2, YU Liujiang2, ZHENG Zhihong2, WANG Xi2, JIANG Zhenbin4. CHEN Anqing4.& XU Jingfang3 1. Department of Physics, East china Normal University, shanghai 200062, china 2. Ion Beam Lab, shanghai Institute of Mini-system and information, Chinese Academy of Sciences,shanghai 200050, china 3. Department of Electronics, School of Information Science and technology, East china Normal Univer- sity, shanghai 200062, china 4. shanghai Cardiovascular Institute, Zhongshan Hospital, shanghai 200032, china Department of Physics East China Normal University Shanghai China Ion Beam Lab Shanghai Institute of Mini-system and information Chinese Academy of Sciences Shanghai China Department of Electronics School of Information Science and Technology East China Normal University Shanghai China shanghai Cardiovascular Institute Zhongshan Hospital Shanghai China

Heart valve diseases threaten human health. One reliable way to save lives of such patients is to replace the pathologically changed heart valves by artificial ones. Over 2 million patients have received LTI-carbon heart valve’s implantation. However, the thrombosis after the implantation is one of the difficulties that need to be solved. In order to improve the blood compatibility and security of mechanical heart valves, ion beam technology was used to modify the surface properties of the materials. The investigation results have been summarized in this paper.

关键词： artificial heart valve, ion implantation, plasma immersed ion implantation, ion beam enhanced deposition.

Phylogeographic analysis of human papillomavirus 58

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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, {4., china 3 School of Life Sciences, Fudan University, shanghai 2004.3, china Obstetrics and Gynecology Hospital of Fudan University Shanghai China shanghai Bio-information Research Center Shanghai China School of Life Sciences Fudan University Shanghai China

Human papillomavirus 58 (HPV58) is one type of HPV with high risk of causing cervical cancer. Unusually high prevalence of HPV58 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 HPV58 high-incidence nations and regions, like china's Mainland, a comprehensive analysis of the global geographical distribution of HPV58 remains blank so far. In this study, HPV58 from the human cervical cancer tissue was detected in china's Mainland, and 14.new HPV58-E6/L1 gene sequences were obtained. Moreover, phylogeographic analysis has been conducted combining the HPV58 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 HPV58 variant, while china's Mainland and Southeast Asia are "transit points" and the new sources of HPV58 after receiving the isolates from the "root" source; like HPV16 and HPV18, the HPV58 might also be one of the major HPV types associated with the development and spread of cervical cancer.

关键词： human papillomavirus 58 (HPV58) cervical cancer phylogeography molecular evolution