Shavit Yoli, Merelli Ivan, Milanesi Luciano, Lio' Pietro
Brief Bioinform. 2016 Sep;17(5):733-44. doi: 10.1093/bib/bbv085. Epub 2015 Oct 3.
Chromosome conformation capture techniques are producing a huge amount of data about the architecture of our genome. These data can provide us with a better understanding of the events that induce critical regulations of the cellular function from small changes in the three-dimensional genome architecture. Generating a unified view of spatial, temporal, genetic and epigenetic properties poses various challenges of data analysis, visualization, integration and mining, as well as of high performance computing and big data management. Here, we describe the critical issues of this new branch of bioinformatics, oriented at the comprehension of the three-dimensional genome architecture, which we call 'Nucleome Bioinformatics', looking beyond the currently available tools and methods, and highlight yet unaddressed challenges and the potential approaches that could be applied for tackling them. Our review provides a map for researchers interested in using computer science for studying 'Nucleome Bioinformatics', to achieve a better understanding of the biological processes that occur inside the nucleus.
染色体构象捕获技术正在产生大量有关我们基因组结构的数据。这些数据能让我们更好地理解从三维基因组结构的微小变化引发细胞功能关键调控的事件。生成关于空间、时间、遗传和表观遗传特性的统一视图，在数据分析、可视化、整合与挖掘以及高性能计算和大数据管理方面带来了各种挑战。在此，我们描述了这一生物信息学新分支的关键问题，其旨在理解三维基因组结构，我们称之为“核基因组生物信息学”，超越了当前可用的工具和方法，并强调了尚未解决的挑战以及可用于应对这些挑战的潜在方法。我们的综述为有兴趣利用计算机科学研究“核基因组生物信息学”以更好理解细胞核内发生的生物学过程的研究人员提供了一张路线图。
