空间转录组学的导航:计算方法如何指引方向。

IF 6.4 2区 生物学 Q1 CELL BIOLOGY Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-03-01 DOI:10.1002/wrna.1839
Runze Li, Xu Chen, Xuerui Yang
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引用次数: 0

摘要

空间分辨转录组学极大地改变了各个领域的生物和医学研究。它能以单细胞、多细胞或亚细胞分辨率进行转录组分析,同时保留复杂组织中细胞的几何定位信息。细胞空间信息及其分子特征的耦合产生了一种新的多模式高通量数据源,为数据挖掘分析方法的开发带来了新的挑战。空间转录组数据往往高度复杂、噪声大、有偏差,给数据分析和生物洞察力的产生带来了一系列困难,其中许多问题尚未解决。此外,为了跟上不断发展的空间转录组实验技术的步伐,现有的分析理论和工具也需要进行相应的更新和改革。在这篇综述中,我们概述并讨论了当前挖掘空间转录组学数据的计算方法。我们提出了方法设计的未来方向和前景,以促进新分析模型和算法的进一步讨论和进步。本文归类于RNA 方法 > 细胞中的 RNA 分析 RNA 进化与基因组学 > RNA 的计算分析 RNA 导出与定位 > RNA 定位。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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Navigating the landscapes of spatial transcriptomics: How computational methods guide the way.

Spatially resolved transcriptomics has been dramatically transforming biological and medical research in various fields. It enables transcriptome profiling at single-cell, multi-cellular, or sub-cellular resolution, while retaining the information of geometric localizations of cells in complex tissues. The coupling of cell spatial information and its molecular characteristics generates a novel multi-modal high-throughput data source, which poses new challenges for the development of analytical methods for data-mining. Spatial transcriptomic data are often highly complex, noisy, and biased, presenting a series of difficulties, many unresolved, for data analysis and generation of biological insights. In addition, to keep pace with the ever-evolving spatial transcriptomic experimental technologies, the existing analytical theories and tools need to be updated and reformed accordingly. In this review, we provide an overview and discussion of the current computational approaches for mining of spatial transcriptomics data. Future directions and perspectives of methodology design are proposed to stimulate further discussions and advances in new analytical models and algorithms. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Evolution and Genomics > Computational Analyses of RNA RNA Export and Localization > RNA Localization.

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来源期刊
CiteScore
14.80
自引率
4.10%
发文量
67
审稿时长
6-12 weeks
期刊介绍: WIREs RNA aims to provide comprehensive, up-to-date, and coherent coverage of this interesting and growing field, providing a framework for both RNA experts and interdisciplinary researchers to not only gain perspective in areas of RNA biology, but to generate new insights and applications as well. Major topics to be covered are: RNA Structure and Dynamics; RNA Evolution and Genomics; RNA-Based Catalysis; RNA Interactions with Proteins and Other Molecules; Translation; RNA Processing; RNA Export/Localization; RNA Turnover and Surveillance; Regulatory RNAs/RNAi/Riboswitches; RNA in Disease and Development; and RNA Methods.
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