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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 center for bioinformation technology,shanghai 200235,china 3 College of Life Science and technology,shanghai Jiaotong University,shanghai 200030,china 4 bioinformation center of shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,shanghai 200031,china Institute of Micro/Nano Science and technology Shanghai Jiaotong UniversityShanghai 200030 China shanghai center for bioinformation technology Shanghai 200235 China College of Life Science and technology Shanghai Jiaotong UniversityShanghai 200030 China bioinformation center of shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200031 China

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

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 bioinformation 1 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 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

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 430074, 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.

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

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 200240,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 400016,china School of Life Science & technology Shanghai Jiaotong UniversityShanghai 200240 China shanghai center for bioinformation and technologyshanghai 200235 China Logistical Engineering UniversityChongqing 400016 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

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 200235,china 1shanghai-MOST Key Laboratory for Disease and Health Genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China. 2Lab 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. 4School of Life Sciences Fudan University Shanghai 200433 China. 5shanghai 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

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 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

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 100052, china 4. bioinformation center, shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, shanghai 200031, china 5. shanghai center for bioinformation technology, shanghai 200235, china 6. School of Life Sciences, Fudan University, shanghai 200433, china 1Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences 100093 Beijing China. 2College of Life Sciences Beijing Normal University 100875 Beijing China. 3Institute of Viral Disease Control and Prevention Chinese CDC 100052 Beijing China. 4bioinformation center Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 200031 Shanghai China. 5shanghai center for bioinformation technology 200235 Shanghai China. 6School of Life Sciences Fudan University 200433 Shanghai China.

The genome organization and expression strategy of severe acute respiratory syndrome coronavirus (SARSCoV) have been described extensivelyl1- 10]. 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[11]. Previous studies suggested that amino acid replacements in the spike protein could dramatically alter the pathogenesis and virulence of some coronaviruses[11]. 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[10], might make this pathogen adapt to a new host. In this study, we investigated a total of 108complete sequences of the SARS-CoV S gene from GenBank (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[13]. Then, we reconstructed the most recent common ancestor (MRCA) sequences of the SARS-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