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With the recent developments in proteomic technologies, a complete human proteome project (HPP) appears feasible for the first time. However, there is still debate as to how it should be designed and what it should encompass. In “proteomics speak”, the debate revolves around the central question as to whether a gene‐centric or a protein‐centric proteomics approach is the most appropriate way forward. In this paper, we try to shed light on what these definitions mean, how large‐scale proteomics such as a HPP can insert into the larger omics chorus, and what we can reasonably expect from a HPP in the way it has been proposed so far. 相似文献
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系统生物学——生命科学的新领域 总被引:14,自引:0,他引:14
系统生物学是继基因组学、蛋白质组学之后一门新兴的生物学交叉学科,代表21世纪生物学的未来.最近,系统生物学研究机构纷纷成立.在研究上,了解一个复杂的生物系统需要整合实验和计算方法.基因组学和蛋白质组学中的高通量方法为系统生物学发展提供了大量的数据.计算生物学通过数据处理、模型构建和理论分析,成为系统生物学发展的一个必不可缺、强有力的工具.在应用上,系统生物学代表新一代医药开发和疾病防治的方向. 相似文献
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Christina Ludwig George Rosenberger Sabine Amon Ben C Collins Ruedi Aebersold 《Molecular systems biology》2018,14(8)
Many research questions in fields such as personalized medicine, drug screens or systems biology depend on obtaining consistent and quantitatively accurate proteomics data from many samples. SWATH‐MS is a specific variant of data‐independent acquisition (DIA) methods and is emerging as a technology that combines deep proteome coverage capabilities with quantitative consistency and accuracy. In a SWATH‐MS measurement, all ionized peptides of a given sample that fall within a specified mass range are fragmented in a systematic and unbiased fashion using rather large precursor isolation windows. To analyse SWATH‐MS data, a strategy based on peptide‐centric scoring has been established, which typically requires prior knowledge about the chromatographic and mass spectrometric behaviour of peptides of interest in the form of spectral libraries and peptide query parameters. This tutorial provides guidelines on how to set up and plan a SWATH‐MS experiment, how to perform the mass spectrometric measurement and how to analyse SWATH‐MS data using peptide‐centric scoring. Furthermore, concepts on how to improve SWATH‐MS data acquisition, potential trade‐offs of parameter settings and alternative data analysis strategies are discussed. 相似文献
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化学基因组学和化学蛋白质组学作为后基因组时代的新技术,是以化学小分子为工具,对细胞的生理过程进行精确干扰,研究有机体和细胞的功能,同时也是新药开发的重要手段。本文综述了化学基因组学和化学蛋白质组学征自噬相关靶点的特异性小分子的发现,及小分子存自噬机理研究中的应用。 相似文献
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Machine learning in bioinformatics 总被引:1,自引:0,他引:1
Larrañaga P Calvo B Santana R Bielza C Galdiano J Inza I Lozano JA Armañanzas R Santafé G Pérez A Robles V 《Briefings in bioinformatics》2006,7(1):86-112
This article reviews machine learning methods for bioinformatics. It presents modelling methods, such as supervised classification, clustering and probabilistic graphical models for knowledge discovery, as well as deterministic and stochastic heuristics for optimization. Applications in genomics, proteomics, systems biology, evolution and text mining are also shown. 相似文献
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Soloviev M Finch P 《Journal of chromatography. B, Analytical technologies in the biomedical and life sciences》2005,815(1-2):11-24
Characterisation of the complement of expressed proteins from a single genome is a central focus of the evolving field of proteomics. Traditional proteomics technologies were developed in the 20th century and are based on two-dimensional electrophoresis or multidimensional liquid chromatography. These facilitated functional genomics analysis, but they currently represent a significant bottleneck to progress in this area. We are now witnessing the development of novel alternative technologies for use in expression proteomics research. This review aims to familiarise the reader with the principles underlying the peptidomics approaches to proteomics research and provide examples of their applications. 相似文献
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功能基因组学的研究方法 总被引:10,自引:1,他引:9
基因组学的研究已从结构基因组学转向功能基因组学,功能基因组学时代对于基因功能的研究也由单一基因转向大规模,批量分析,本综述了功能基因组学的研究内容与方法,主要包括:差异显示反转录PCR,基因表达序列分析(SAGE),微点阵,遗传足迹法,反求遗传学,蛋白质组学和生物信息学等新方法。 相似文献
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Recent improvements in proteomic technologies have collectively yielded data sets that far exceed the capabilities of typical low‐throughput interpretation strategies. Unfortunately, tools designed to leverage the “peptide‐centric” content of MS‐based proteomics lag the current rate of data production. Here, we describe Pathway Palette ( http://blaispathways.dfci.harvard.edu ), a freely accessible internet application that enables researchers to easily transition from peptides to biological pathways, while simultaneously retaining the qualitative and quantitative aspects of the underlying MS data. 相似文献
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丝状真菌不仅是致病菌,而且在异源表达工业酶、化学制品以及药物活性物质中发挥着越来越重要的作用。随着人类基因组计划的实施和推进,生命科学研究已进入了功能基因组时代,特别是蛋白质组学,在蛋白质水平对丝状真菌细胞生命过程中蛋白质功能和蛋白质之间的相互作用以及特殊条件下的变化机制进行研究,对生命的复杂活动进行深入而又全面的认识也为丝状真菌工业酶制剂和重组药物的开发提供广阔的创新空间。本文综述了蛋白质组学的研究内容和方法,总结了其在丝状真菌致病菌、抗生素产生菌和纤维素酶产生菌中的应用现状。不同层次的功能基因组学分析可以从各个角度掌握生物体的代谢网络和调控机制,本文还对蛋白质组学以及功能基因组学各部分内容的整合运用进行了展望。 相似文献
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Parkinson's disease (PD) is a complex neurological disorder, characterized by selective degeneration of nigrostriatal dopaminergic neurons. It is a multi-factorial disease, contributed by a combination of age, genetic and environmental factors. Etiology of sporadic PD and mechanism underlying selective loss of dopaminergic neurons has not yet been clearly understood. Recent developments in genomics and proteomics have revolutionized the research on PD at genetic level. Differential gene expression patterns (DNA biochip technology), age-dependent complex genetic patterns (SNP genotyping), and protein expression profiles (proteomics) of PD patients have started providing the specific and rigorous molecular explanation and role of modifying factors in PD. Genomics and proteomics are further expected to help in developing biomarkers for diagnosis of early onset PD and also to develop valuable and potential therapeutic strategies for its treatment. In this review, we have discussed the progress made by genomics and proteomics, in understanding the role of modifying factors in PD. 相似文献
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Large-scale protein quantification has become a major proteomics application in many areas of biological and medical research.
During the past years, different techniques have been developed, including gel-based such as differential in-gel electrophoresis
(DIGE) and liquid chromatography-based such as isotope labeling and label-free quantification. These quantitative proteomics
tools hold significant promise for biomarker discovery, diagnostic and therapeutic applications. They are also important for
research in functional genomics and systems biology towards basic understanding of molecular networks and pathway interactions.
In this review, we summarize current technologies in quantitative proteomics and discuss recent applications of the technologies. 相似文献
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Christina Holmes Siobhan M. Carlson Fiona McDonald Mavis Jones Janice Graham 《New genetics and society》2016,35(1):49-68
Richard Lewontin proposed that the ability of a scientific field to create a narrative for public understanding garners it social relevance. This article applies Lewontin's conceptual framework of the functions of science (manipulatory and explanatory) to compare and explain the current differences in perceived societal relevance of genetics/genomics and proteomics. We provide three examples to illustrate the social relevance and strong cultural narrative of genetics/genomics for which no counterpart exists for proteomics. We argue that the major difference between genetics/genomics and proteomics is that genomics has a strong explanatory function, due to the strong cultural narrative of heredity. Based on qualitative interviews and observations of proteomics conferences, we suggest that the nature of proteins, lack of public understanding, and theoretical complexity exacerbates this difference for proteomics. Lewontin's framework suggests that social scientists may find that omics sciences affect social relations in different ways than past analyses of genetics. 相似文献
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本文系统地介绍了环境基因组学的基本概念和主流技术平台,及其在环境污染控制、健康风险检测与评价等方面地应用.并阐释了环境基因组学与环境蛋白组学、生物信息学之间的关系。环境基因组学在生物基因组水平上揭示了环境污染物与生物之间的相互作用,为维护人体与环境健康,进行分子水平遗传物质的检测与调控。奠定了理论基础与技术支持,目前已经成为控制环境污染,提高人体与环境健康质量的重要议题。 相似文献
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Maize, sorghum, sugarcane, switchgrass and miscanthus are the main crops suggested as potential sources of lignocellulosic biomass for the production of second‐generation ethanol. The attention these crops have received has been concentrated in the field of genomics, and very little research has been performed in the field of proteomics, particularly in the cell wall proteomic, despite the importance of these crops in biofuel production. New mass spectrometry‐based proteomic methods allow the identification and quantification of thousands of proteins in complex mixtures, as well as the detection of post‐translational changes in complex proteomes, providing important insight into the downstream consequences of gene expression. Together with other ‘omic’ approaches, proteomic might be decisive to bring new information in the study of cell wall formation. Here, we briefly highlight proteomic techniques and review the research that has been completed on the proteomes of these five crops. 相似文献