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SySAP: a system-level predictor of deleterious single amino acid polymorphisms

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Protein & Cell 2012年第1期3卷 38-43页

作者： Tao Huang Chuan Wang Guoqing Zhang Lu Xie Yixue Li Key Laboratory of Systems Biology Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200031China shanghai center for bioinformation Technology Shanghai 200235China

Single amino acid polymorphisms(SAPs),also known as non-synonymous single nucleotide polymorphisms(nsSNPs),are responsible for most of human genetic *** the deleterious SAPs from neutral ones can help identify the disease genes and understand the mechanism of *** this work,a method of deleterious SAP prediction at system level was *** most existing methods,our method not only considers the sequence and structure information,but also the network *** integration of network information can improve the performance of deleterious SAP *** make our method available to the public,we developed SySAP(a System-level predictor of deleterious Single Amino acid Polymorphisms),an easy-to-use and high accurate web *** is freely available at http://***/SySAP/and http://***/SySAP/.

关键词： deleterious single amino acid polymorphisms predictor web server

维普期刊数据库

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

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

作者： WU WEI~(1,3#), Weihua WANG~(2#), Zhiwei CAO~(3#), Hong YU~3, Xiaojing WANG~1, Jing ZHAO~3, Hao TAN~3, Hao XU~3, Weihong JIANG~(2*), and Yixue LI~(1,3*) 1 bioinformation center, Key Lab of Systems Biology, shanghai institutes for biological sciences, Chinese Academy of sciences, Graduate School of the Chinese Academy of sciences, shanghai 200031, China 2 Laboratory of Molecular Microbiology, Institute of Plant Physiology and Ecology, shanghai institutes for biological sciences, Chinese Academy of sciences, Graduate School of the Chinese Academy of sciences, shanghai 200032, China 3 shanghai center for bioinformation Technology, shanghai 200235, China bioinformation center Key Lab of Systems Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200031 China shanghai center for bioinformation Technologyshanghai 200235 China Laboratory of Molecular Microbiology Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200032 China

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

Analysis and application of large-scale protein-protein interaction data sets

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Chinese Science Bulletin 2005年第20期50卷 2267-2272页

作者： SUN Jingchun XU Jinlin LI Yixue SHI Tieliu School of Life sciences & Technology Shanghai Jiaotong University Shanghai 200240 China bioinformation center Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China

Protein-protein interactions play key roles in cells. Lots of experimental approaches and in silico methods have been developed to identify and predict large-scale pro- tein-protein interactions. However, compared with the tradi- tionally experimental results, the high-throughput pro- tein-protein interaction data often contain the false positives in high probability. In order to fully utilize the large-scale data, it is necessary to develop bioinformatic methods for systematically evaluating those data in order to further im- prove the data reliability and mine biological information. This review summarizes the methodologies of analysis and application of high-throughput protein-protein interaction data, including the evaluation methods, the relationship be- tween protein-protein interaction data and other protein biological information, and their applications in biological study. In addition, this paper also suggests some interesting topics on mining high-throughput protein-protein interaction data.

关键词：蛋白质交互作用生物学功能预测生物途径

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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RNA m^(6)A reader YTHDF2 facilitates precursor miR-126 maturation to promote acute myeloid leukemia progression

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Genes & Diseases 2024年第1期11卷 382-396页

作者： Zheng Zhang Keren Zhou Li Han Andrew Small Jianhuang Xue Huilin Huang Hengyou Weng Rui Su Brandon Tan Chao Shen Wei Li Zhicong Zhao Ying Qing Xi Qin Kitty Wang Keith Leung Mark Boldin Chun-Wei Chen David Ann Zhijian Qian Xiaolan Deng Jianjun Chen Zhenhua Chen Department of Systems Biology Beckman Research Institute of City of HopeMonroviaCA 91016USA Irell and Manella Graduate School of biological sciences Beckman Research Institute of City of HopeDuarteCA 91010USA Gehr Family center for Leukemia Research City of HopeDuarteCA 91010USA Sun Yat-sen University Cancer center State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangzhouGuangdong 510060China Guangzhou Laboratory GuangzhouGuangdong 510005China Bioland Laboratory GuangzhouGuangdong 51005China Department of Liver Surgery Renji HospitalShanghai Jiao Tong University School of MedicineShanghai 200127China Department of Diabetes Complications and Metabolism Beckman Research Institute of City of HopeDuarteCA 91010USA Department of Biochemistry and Molecular Biology University of FloridaGainesvilleFL 32603USA Tongji Hospital Affiliated to Tongji University Frontier Science Center for Stem Cell ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghai 200092China School of Pharmacy China Medical UniversityShenyangLiaoning 110001China

As the most common internal modification of mRNA,Ne-methyladenosine(m^(6)A)and its regulators modulate gene expression and play critical roles in various biological and patholog-ical processes including *** was reported previously that m^(6)A methyltransferase(writer),methyltransferase-like 3(METTL3)adds m^(6)A in primary microRNAs(pri-miRNAs)and fa-cilitates its processing into precursor miRNAs(pre-miRNAs).However,it is unknown whether m^(6)A modification also plays a role in the maturation process of pre-miRNAs and(if so)whether such a function contributes to ***,we found that YTHDF2 is aberrantly overexpressed in acute myeloid leukemia(AML)patients,especially in relapsed patients,and plays an onco-genic role in ***,YTHDF2 promotes expression of miR-126-3p(also known as miR-126,as it is the main product of precursor miR-126(pre-miR-126)),a miRNA that was reported as an oncomiRNA in AML,through facilitating the processing of pre-miR-126 into mature ***,YTHDF2 recognizes m^(6)A modification in pre-miR-126 and recruits AGO2,a regulator of pre-miRNA processing,to promote the maturation of ***2 posi-tively and negatively correlates with miR-126 and miR-126's downstream target genes,respec-tively,in AML patients,and forced expression of miR-126 could largely rescue YTHDF2/Ythdf2 depletion-mediated suppression on AML cell growth/proliferation and leukemogenesis,indi-cating that miR-126 is a functionally important target of YTHDF2 in ***,our studies not only reveal a previously unappreciated YTHDF2/miR-126 axis in AML and highlight the ther-apeutic potential of targeting this axis for AML treatment,but also suggest that m^(6)A plays a role in pre-miRNA processing that contributes to tumorigenesis.

关键词： AML miR-126 N^(6)-methyladenosine Pre-miRNA maturation YTHDF2

Single-cell omics:experimental workflow,data analyses and applications

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Science China Life sciences 2024年

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biology the Institute of Biomedical Sciences and School of Life Sciences East China Normal University Beijing institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua center for Life sciences Academy for Advanced Interdisciplinary Studies Center for Quantitative Biology (CQB) Peking University Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women’s Hospital Zhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of Statistics East China Normal University Shanghai 200062 China Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics Institute College of Pharmaceutical Sciences Zhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of Education Orthopaedic Department Tongji Hospital Bioinformatics Department School of Life Sciences and Technology Tongji University Frontier Science center for Stem Cells School of Life Sciences and Technology Tongji University Translational Medical center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East Hospital Bioinformatics Department School of Life Sciences and Technology Tongji University Research Institute of Intelligent Computing Zhejiang Lab shanghai Research Institute for Intelligent Autonomous Systems center for Single-cell Omics School of Public Health Shanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River Delta Zhejiang University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

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Genomic investigation and nationwide tracking of pediatric invasive nontyphoidal Salmonella in China

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mLife 2024年第1期3卷 156-160页

作者： Yefang Ke Lin Teng Zhe Zhu Wenbo Lu Wenyuan Liu Haiyang Zhou Qi Yu Lina Ye Pan Zhu Guoping Zhao Min Yue Deparment of Clinical Laboratory Ningbo Women and Children's HospitalNingboChina Department of Veterinary Medicine Zhejiang University Cllege of Animal SciencesHangzhouChina Department of Blood Transfusion Ningbo No.2 HospitalNingboChina Office of Screening Ningbo Women and Children's HospitalNingboChina Neonatal Intensive Care Unit Ningbo Women and Children's HospitalNingboChina School of Life Science Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina CAS Key Laboratory of Synthetic Biology Institute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina Department of Microbiology and Microbial Engineering School of Life SciencesFudan UniversityShanghaiChina State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious DiseasesNational Medical Center for Infectious DiseasesThe First Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhouChina Hainan Institute of Zhejiang University SanyaChina

Impact Statement。Invasive nontyphoidal Salmonella(iNTS)causes significant concern with~15%morbidity,affecting populations mainly in African countries.

关键词： pediatric nationwide morbidity

TNF receptor-associated factor-2 binding site is involved in TNFR75-dependent enhancement of TNFR55-induced cell death

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Cell Research 2001年第3期11卷 217-222页

作者： LU FANG, JIA FANG, CHANG QING CHEN shanghai Research center of Biotechnology, shanghai institutes for biological sciences the Chinese Academy of sciences, shanghai 200233, China shanghai Research center of Biotechnology Shanghai Institutes for Biological Sciences the Chinese Academy of Sciences Shanghai China

TNF recepter-55 is the main mediator of TNF-induced apoptosis. TNF receptor-75-dependent induction or enhancement of cytotoxicity has been explained by intracellular signaling, 'ligand passing' , or induction of endogenous TNF. To study the function of human TNF receptor-75 (hTR75) and the interaction between human TNF receptor-55 (hTR55) and hTR75 in hTNFa-induced cytotoxicity, HEp-2 cells were transfected with bicistronic expression vector of hTR75 and its deletion mutants genes. hTNFa-induced cytotoxicity was determined by crystal violet colorimetric method. The expression of hTR75 and its deletion mutants in HEp-2 cells was demonstrated by RT-PCR and indirect ELISA. We found that the overexpressed hTR75 could significantly increase the susceptibility of HEp-2 cells to hTNFa which especially required TRAF2 binding site. hTR75 could not only mediate partial hTNFa-induced cytotoxicity independently but also fulfill an accessory role in enhancing or synergizing hTR55-mediated cytotoxicity

关键词： hTNFa hTNF receptors TRAF2 cytotoxcity signal transduction.