Ten computational challenges in human virome studies

Yifan Wu; Yousong Peng

doi:10.1016/j.virs.2024.04.008

December 2024

. doi: 10.1016/j.virs.2024.04.008

Citation: Yifan Wu, Yousong Peng. Ten computational challenges in human virome studies .VIROLOGICA SINICA, 2024, 39(6) : 845-850. http://dx.doi.org/10.1016/j.virs.2024.04.008

人体病毒组研究中的十个计算生物学问题

吴一凡 ,
彭友松 ^,

cstr: 32224.14.j.virs.2024.04.008

湖南大学生物学院, 长沙 410082

通讯作者： 彭友松, pys2013@hnu.edu.cn
收稿日期： 2024-01-10
录用日期： 2024-04-25

摘要

近年来，针对人体病毒组的多样性以及病毒组在人类健康和疾病中错综复杂的作用方面的研究取得了重大进展。然而，相比宏基因组研究，人体病毒组研究仍处于初期阶段，其中最重要的一个原因是缺乏有效的方法，特别是计算方面的方法。本文系统地概述了病毒组学研究中涉及的十个计算生物学方面的挑战。造成这些挑战的原因多样，包括病毒组的巨大多样性、病毒基因组中缺乏通用标记基因、病毒群体的低丰度、病毒蛋白与已知蛋白的远同源性、病毒组的高度动态和异质性等等。针对每个挑战，我们讨论了其产生原因、当前研究进展以及潜在解决思路。我们认为解决这些挑战需要计算生物学、病毒学和其他多个跨学科研究人员之间的持续合作。总的来说，本论文可以作为人体病毒组研究中的计算生物学研究指南。
- 人类病毒组
- , 计算生物学
- , 计算病毒组学
- , 人工智能

Ten computational challenges in human virome studies

Yifan Wu ,
Yousong Peng ^,

Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China

Corresponding author: Yousong Peng, pys2013@hnu.edu.cn
Received Date: 10 January 2024
Accepted Date: 25 April 2024

Abstract

In recent years, substantial advancements have been achieved in understanding the diversity of the human virome and its intricate roles in human health and diseases. Despite this progress, the field of human virome research remains nascent, primarily hindered by the lack of effective methods, particularly in the domain of computational tools. This perspective systematically outlines ten computational challenges spanning various types of virome studies. These challenges arise due to the vast diversity of viromes, the absence of a universal marker gene in viral genomes, the low abundance of virus populations, the remote or minimal homology of viral proteins to known proteins, and the highly dynamic and heterogeneous nature of viromes. For each computational challenge, we discuss the underlying reasons, current research progress, and potential solutions. The resolution of these challenges necessitates ongoing collaboration among computational scientists, virologists, and multidisciplinary experts. In essence, this perspective serves as a comprehensive guide for directing computational efforts in human virome studies.
- Human virome
- , Computational biology
- , Computational viromics
- , Artificial intelligence

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