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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

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 center for bioinformation and technology,shanghai 200235,china 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

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

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

2023 Chinese national clinical practice guideline on diagnosis and management of Crohn’s disease

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中华医学杂志(英文版) 2024年第14期137卷 2024 Jul 2页

作者： Inflammatory Bowel Disease Group, Chinese Society of Gastroenterology, Chinese Medical Association Inflammatory Bowel Disease Quality Control center of china Xijing Hospital Air Force Medical University China Peking Union Medical College Hospital China West china Hospital Sichuan University China The First Affiliated Hospital Dalian Medical University China University of Nottingham Ningbo China GRADE Centre United Kingdom The First Affiliated Hospital Sun Yat-sen University China Sir Run Run Shaw Hospital Zhejiang University School of Medicine China Peking University People's Hospital China The Second Affiliated Hospital Zhejiang University School of Medicine China Renmin Hospital Wuhan University China Chinese PLA General Hospital China The First Affiliated Hospital Naval Medical University China The Sixth Affiliated Hospital Sun Yat-sen University China The First Affiliated Hospital Anhui Medical University China Zhongshan Hospital Xiamen University China Zhongnan Hospital Wuhan University China The First Hospital of Shanxi Medical University China The Eighth Affiliated Hospital Sun Yat-sen University China Peking University Third Hospital China Peking University First Hospital China Qilu Hospital Shandong University China General Hospital of Eastern Theater Command China Xiangya Hospital Central South University China The Tenth People's Hospital Tongji University China The First Affiliated Hospital Kunming Medical University China shanghai Pudong New District Zhoupu Hospital China Ruijin Hospital Shanghai Jiao Tong University School of Medicine China Tongji Medical College Huazhong University of Science and Technology China General Hospital of Nanjing Military Command China The Third Xiangya Hospital Central South University China Daping Hospital Chongqing China The Second Xiangya Hospital Central South University China Jiangsu Provincial People's Hospital China The Second Hospital of Hebei Medical University China Nanjing Drum Tower Hospital China Nanfan Hospital Southern Medical University China GRADE center University of Nottingham Ningbo China The Fifth Affiliated Hospital Zhengzhou University

The role of Chinese expert consensus in standardization and improvement of the clinical diagnosis and treatment of inflammatory bowel disease (IBD) is self-evident. As clinical and basic research in china becomes standardized under a better understanding of IBD, more data on Chinese patients have become available to develop a consensus and guideline. This guideline, collaboratively developed by the IBD Group, Chinese Society of Gastroenterology, incorporates the latest international consensus statements,[1-7] domestic research findings, and practical considerations, as an update based on the 2018 Chinese consensus on IBD management.[8] The IBD guideline consists of two parts: ulcerative colitis (UC) and Crohn's disease, and this manuscript presented the UC part. The evidence used in this guideline was collected and analyzed by the standard of guideline, and the contents were organized as problem statements, for clarity. The formulation of this guideline aimed to reflect the latest progress in IBD, providing comprehensive and valuable guidance for the clinical management of IBD.

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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 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.

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

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, shanghai 200235, china 3 School of Life Sciences, Fudan University, shanghai 200433, 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

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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 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

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Chinese expert consensus on refined diagnosis,treatment,and management of advanced primary liver cancer(2023 edition)

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