在线工具在营养科学中的生物信息学分析。
Online tools for bioinformatics analyses in nutrition sciences.
机构信息
Department of Nutrition and Health Sciences, University of Nebraska, Lincoln, Nebraska, USA.
出版信息
Adv Nutr. 2012 Sep 1;3(5):654-65. doi: 10.3945/an.112.002477.
Abstract
Recent advances in "omics" research have resulted in the creation of large datasets that were generated by consortiums and centers, small datasets that were generated by individual investigators, and bioinformatics tools for mining these datasets. It is important for nutrition laboratories to take full advantage of the analysis tools to interrogate datasets for information relevant to genomics, epigenomics, transcriptomics, proteomics, and metabolomics. This review provides guidance regarding bioinformatics resources that are currently available in the public domain, with the intent to provide a starting point for investigators who want to take advantage of the opportunities provided by the bioinformatics field.
摘要
“组学”研究的最新进展产生了大型数据集，这些数据集是由财团和中心创建的，也有由个别研究人员创建的小型数据集，以及用于挖掘这些数据集的生物信息学工具。营养实验室充分利用分析工具来查询与基因组学、表观基因组学、转录组学、蛋白质组学和代谢组学相关的信息非常重要。本综述提供了有关公共领域当前可用的生物信息学资源的指导，旨在为希望利用生物信息学领域提供的机会的研究人员提供一个起点。
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本文引用的文献
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2
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3
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4
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5
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8
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