Subramanian Devika, Natarajan Jeyakumar
Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, India.
Crit Rev Microbiol. 2023 May;49(3):391-413. doi: 10.1080/1040841X.2022.2065905. Epub 2022 Apr 25.
is a notorious pathogen posing challenges in the medical industry due to drug resistance and biofilm formation. The horizon of knowledge on pathogenesis has expanded with the advancement of data-driven bioinformatics techniques. Mining information from sequenced genomes and their expression data is an economic approach that alleviates wastage of resources and redundancy in experiments. The current review covers how big data bioinformatics has been used in the analysis of from publicly available -omics data to uncover mechanisms of infection and inhibition. Particularly, advances in the past two decades in biomarker discovery, host responses, phenotype identification, consolidation of information, and drug development are discussed highlighting the challenges and shortcomings. Overall, the review summarizes the diverse aspects of scrupulous re-analysis of proteomic and transcriptomic expression datasets retrieved from public repositories in terms of the efforts taken, benefits offered, and follow-up actions. The detailed review thus serves as a reference and aid for (i) Computational biologists by briefing the approaches utilized for bacterial omics re-analysis concerning and (ii) Experimental biologists by elucidating the potential of bioinformatics in biological research to generate reliable postulates in a prompt and economical manner.
是一种臭名昭著的病原体,由于耐药性和生物膜形成,给医疗行业带来了挑战。随着数据驱动的生物信息学技术的进步,关于发病机制的知识视野得到了扩展。从测序基因组及其表达数据中挖掘信息是一种经济的方法,可减少资源浪费和实验冗余。当前的综述涵盖了大数据生物信息学如何用于分析公开可用的组学数据,以揭示感染和抑制机制。特别讨论了过去二十年在生物标志物发现、宿主反应、表型鉴定、信息整合和药物开发方面的进展,突出了挑战和不足。总体而言,该综述从所付出的努力、提供的益处和后续行动等方面,总结了对从公共存储库检索到的蛋白质组学和转录组学表达数据集进行严谨重新分析的不同方面。因此,详细的综述可为以下人员提供参考和帮助:(i)计算生物学家,通过介绍用于细菌组学重新分析的方法;(ii)实验生物学家,通过阐明生物信息学在生物学研究中的潜力,以快速且经济的方式生成可靠的假设。