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Lifeomics leads the age of grand discoveries

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Science China(Life Sciences) 2013年第3期56卷 201-212页

作者： he fuchu State Key Laboratory of Proteomics Beijing Proteome Research CenterNational Center for Protein Science(Beijing)

When our knowledge of a field accumulates to a certain level,we are bound to see the rise of one or more great *** will make a series of grand discoveries/breakthroughs and push the discipline into an 'age of grand discoveries'.Mathematics,geography,physics and chemistry have all experienced their ages of grand discoveries;and in life sciences,the age of grand discoveries has appeared countless times since the 16th *** to the ever-changing development of molecular biology over the past 50 years,contemporary life science is once again approaching its breaking point and the trigger for this is most likely to be 'lifeomics'.At the end of the 20th century,genomics wrote out the 'script of life';proteomics decoded the script;and RNAomics,glycomics and metabolomics came into *** 'omics',with their unique epistemology and methodology,quickly became the thrust of life sciences,pushing the discipline to new ***,which encompasses all omics,has taken shape and is now signalling the dawn of a new era,the age of grand discoveries.

关键词： age of grand discoveries lifeomics life sciences

Progress in study of structure-function relationship and protein engineering of plasminogen activators

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Chinese Science Bulletin 1999年第4期44卷 289-294页

作者： Fuxiang Zhu fuchu he Beijing Inst Radiat Med Beijing 100850 Peoples R China

Thrombolytic agents play an important role in the treatment of thrombus diseases. In clinic,traditional thrombolytic agents always resulted in the side effect of systemic thrombolysis because of the shortcomings, such as short half-life, poor specificity of thrombus. Recently, with the development of knowledge of the relationship between their structure and function, a series of new thrombolytic agents were constructed by means of molecular biological techniques. Developing new types of thrombolytic agents is of great significance for more effective treatment of cardiovascular diseases. The latest knowledge of the structure-function relationship of t-PA and u-PA and the progress in development of new thrombolytic agents are reviewed.

关键词： thrombolytic agents t-PA u-PA variants.

At a glance:Proteomics in China

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Science China(Life Sciences) 2011年第1期54卷 1-2页

作者： he fuchu State Key Laboratory of Proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine Beijing 102206 China

Proteomics is a new science that focuses on the comprehensive analysis of proteins in intact organisms or in molecule machineries, organelles, cells, tissues, or organs. It has become an important area of interests in... 详细信息

关键词：蛋白质组学中国生物科技生命科学细胞器新科学有机体

Bioinformatics, robust realm based upon multidisciplinary knowledge of biological data and computational techniques

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Chinese Science Bulletin 1999年第20期44卷 1825-1837页

作者： Shuguang Ouyang fuchu he Inst Radiat Med Beijing 100850 Peoples R China

The accumulation of the large amount of biological data concerning with gene and protein research has proposed that it is necessary to abstract the biological significance from these data. Then the bioinformatics, equipped with the most advanced computational techniques and supported by the latest biological research, has emerged for this purpose. Some recent information on the developing bioinformatics, associated with the uniform resource location addresses of those available resource sites that support hyper-text or general file transfer proto-

关键词： bioinformatics bioinformation molecular biology computer science Internet.

An overview of human protein databases and their application to functional proteomics in health and disease

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Science China(Life Sciences) 2011年第11期54卷 988-998页

作者： ZHANG YanQiong ZHU YunPing he fuchu Institute of Basic Medical Sciences Chinese Academy of Medical Sciences ＆ Peking Union Medical College Beijing 100730 China State Key Laboratory of Proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine Beijing 102206 China

Functional proteomics can be defined as a strategy to couple proteomic information with biochemical and physiological analyses with the aim of understanding better the functions of proteins in normal and diseased *** recent years,a variety of publicly available bioinformatics databases have been developed to support protein-related information management and biological knowledge *** addition to being used to annotate the proteome,these resources also offer the opportunity to develop global approaches to the study of the functional role of proteins both in health and ***,we present a comprehensive review of the major human protein bioinformatics *** conclude this review by discussing a few examples that illustrate the importance of these databases in functional proteomics research.

关键词： human protein database bioinformatics functional proteomics health disease

Nusap1 is essential for neural crest cell migration in zebrafish

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Protein & Cell 2010年第3期1卷 259-266页

作者： Jing Nie Hua Wang fuchu he Huizhe Huang Department of Biology Sciences and Biotechnology Tsinghua UniversityBeijing 100084China School of Life Sciences Xiamen UniversityXiamen 361005China State Key Laboratory of Proteomics Beijing Proteome Research CenterBeijing Institute of Radiation MedicineBeijing 100850China Institutes of Biomedical Sciences Fudan UniversityShanghai 200032China

Microtubules play important roles in mitotic spindle assembly and chromosome segregation to maintain normal cell cycle progression.A number of microtubule-associated proteins have been identified in epithelial and neural cell cultures;however,their physiological significance is not well characterized due to the lack of appropriate in vivo animal *** spindleassociated protein(NuSAP)is a microtubule-binding protein and is reported to be involved in mitosis by cell culture *** this report,we identified the zebrafish homologue of human NuSAP and investigated its expression profile and *** in situ hybridization,we demonstrated that transcripts of zebrafish nusap1 are specifically expressed in the retina,forebrain,hindbrain and neural *** the in vivo expression of nusap1 was knocked down through antisense oligonucleotide morpholino technology,the morphants of nusap1 showed impaired morphogenesis in the trunk and yolk extension,implying the involvement of Nusap1 in cell *** studies revealed that nusap1 morphants have an altered expression pattern of neural crest markers crestin and sox9b,but normal expression of blood vessel and notochord markers gata1 and *** addition,nusap1 mRNA injection caused serious apoptosis in retina and hindbrain tissue,and these phenotypes can be rescued by co-injection of morpholino against *** observations not only suggest a role for Nusap1 in connecting apoptosis with cell migration,but also provide strong evidences that Nusap1 is potentially involved in morphogenesis in vertebrates.

关键词： Nusap1 zebrafish microtubule apoptosis migration neural crest

Comprehensive Profiling for Histone H4 of Human Liver Cells Using High Resolution LTQ-Orbitrap Mass Spectrometry

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Chinese Journal of Chemistry 2011年第1期29卷 171-177页

作者： Nie, Aiying LU, Haojie Yang, Pengyuan he, fuchu Department of Chemistry and Institute of Biomedical Sciences Fudan University Shanghai 200433 China State Key Laboratory ofProteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine Beijing 102206 China

The post translational modifications of histone variants are playing an important role in the structure of chromatin, the regulation of gene activities and the diagnosis of diseases, and conducting in-depth researches and discovering new sites depend on new and rational analytical methods to some extent. In this work, the combinatorial method of high resolution LTQ-Orbitrap mass spectrometry and multiple enzymes was employed to identify the post translational modifications （PTMs） of histone H4 of human liver cells. The novel methylation site, argnine 67 （R 67）, was observed besides some sites reported previously such as lysine 31 （K 31）, lysine 44 （K 44）, argnine 55 （R 55） and lysine 59 （K 59） in the global domain. Meanwhile, various combinations of acetylation of lysine 5 （K 5）, lysine 8 （K 8）, lysine 12 （K 12）, lysine 16 （K 16） and methylation of lysine 20 （K 20） in the NH2-terminal tails were also identified after the LC-MS/MS analysis of trypsin, Arg-C, Glu-C and chymotrypsin digests.

关键词： histone post translational modification mass spectrometry enzymes

Path PPI: an integrated dataset of human pathways and protein-protein interactions

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Science China(Life Sciences) 2015年第6期58卷 579-589页

作者： TANG HaiLin ZHONG Fan LIU Wei he fuchu XIE HongWei College of Mechanical & Electronic Engineering and Automatization National University of Defense Technology Institutes of Biomedical Sciences Fudan University State Key Laboratory of Proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine

Integration of pathway and protein-protein interaction(PPI) data can provide more information that could lead to new biological insights. PPIs are usually represented by a simple binary model, whereas pathways are represented by more complicated models. We developed a series of rules for transforming protein interactions from pathway to binary model, and the protein interactions from seven pathway databases, including PID, Bio Carta, Reactome, Net Path, INOH, SPIKE and KEGG, were transformed based on these rules. These pathway-derived binary protein interactions were integrated with PPIs from other five PPI databases including HPRD, Int Act, Bio GRID, MINT and DIP, to develop integrated dataset(named Path PPI). More detailed interaction type and modification information on protein interactions can be preserved in Path PPI than other existing datasets. Comparison analysis results indicate that most of the interaction overlaps values(OAB) among these pathway databases were less than 5%, and these databases must be used conjunctively. The Path PPI data was provided at http://proteomeview. ***/Path PPI/Path ***.

关键词： databases integration pathway protein-protein interaction proteomics

Forum on frontiers of science and technology:Lifeomics and translational medicine

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Science China(Life Sciences) 2013年第3期56卷 199-200页

作者： QIANG BoQin he fuchu ZENG YiXin State Key Laboratory of Medical Molecular Biology Institute of Basic Medical SciencesChinese Academy of Medical Sciences State Key Laboratory of Proteomics Beijing Proteome Research CenterNational Center for Protein Sciences(Beijing) State Key Laboratory of Medical Molecular Biology Chinese Academy Of Medical SciencesPeking Union Medical College

The Chinese Academy of Sciences held its 7th forum on frontiers of Science and Technology, April 12-13, 2012, in the academy hall of the Chinese Academy of Sciences. The Forum was organized by the Life Science and Medicine Division and co-organized by Academy of Military Medical Sciences and Science China Press. The theme of the 7th Forum was ＂Lifeomics and Translational Medicine＂,

关键词：军事医学论坛转化中国社科院科技生命科学科学出版社科学院