下一篇 病毒:使用基因组模型对致瘤病毒进行分类
John Robertson1, Shorya Consul1, Haris Vikalo1
1Chandra Family Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas, United States of America.
PLoS computational biology
|August 21, 2025
概括
在癌症样本中精确地分类瘤病毒DNA. 这种基因组基础模型框架提高了多种病毒物种的检测,改善了癌症研究和诊断.
科学领域:
- 基因组学
- 生物信息学
- 癌症学
背景情况:
- 瘤病毒是与癌症发展有关的病原体.
- 在瘤样本中检测瘤病毒对于癌症研究至关重要.
- 目前的方法在单个样本中对抗多种瘤病毒.
研究的目的:
- 开发一个精确的病毒分类的计算框架.
- 适应基因组基础模型进行瘤病毒检测.
- 在瘤DNA中识别多种瘤病毒的挑战.
主要方法:
- 推出了NextVir,一个多类病毒分类框架.
- 适应的基因组基础模型 (DNABERT-S,核酸转换器,HyenaDNA).
- 精细调整的模型用于精确的测序读取来源识别.
主要成果:
- 与现有的深度学习方法相比,NextVir表现出卓越的性能.
- 该框架准确地识别了各种瘤病毒的序列阅读.
- 在模拟瘤样本中成功分类多种瘤病毒.
结论:
- 基因组基础模型显示了基因组学和癌症研究的巨大潜力.
- NextVir为复杂的病毒检测提供了强大的解决方案.
- 这种框架可以进一步了解与病毒相关的癌症.
相关概念视频
Mechanisms of Retrovirus-induced Cancers
5.3K
Retroviruses are RNA viruses that have been shown to cause cancers in diverse species, including chickens, mice, cats, and monkeys. The RNA genomes of these viruses are first reverse-transcribed into single and then double-stranded DNA (dsDNA) copies. This dsDNA called proviral DNA then integrates into the host genome. Subsequently, the host cell transcribes the proviral DNA in concert with the chromosomal DNA. This leads to the production of viral RNA and proteins that assemble at the host...
5.3K
Rous Sarcoma Virus (RSV) and Cancer
5.4K
Rous Sarcoma virus or RSV was discovered by F. Peyton Rous in the year 1911 as a filterable transmissible agent that could cause tumors in chickens. He won a Nobel Prize for this discovery in 1966. His experiments clearly demonstrated that some cancers could be caused by infectious agents and led to the discovery of many more cancer-causing viruses in animals as well as humans.
RSV is a retrovirus that contains two copies of a plus-strand RNA genome. Its genome consists of four main open...
RSV is a retrovirus that contains two copies of a plus-strand RNA genome. Its genome consists of four main open...
5.4K
Retroviruses
12.7K
Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
12.7K
Viruses with RNA Genomes
118
RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
118
Introduction to Virus
206
Viruses are unique biological entities that blur the boundary between living and non-living systems. Although they lack cellular structure and metabolic processes, they can exhibit characteristics of life when infecting a host. Their defining feature is a nucleic acid core, composed of either DNA or RNA, encapsulated within a protein coat called a capsid. This simple structure allows them to invade host cells and use their machinery for replication efficiently.Viral Structure and...
206
Viral Structure
63.6K
Viruses are extraordinarily diverse in shape and size, but they all have several structural features in common. All viruses have a core that contains a DNA- or RNA-based genome. The core is surrounded by a protective coat of proteins called the capsid. The capsid is composed of subunits called capsomeres. The capsid and genome-containing core are together known as the nucleocapsid.
63.6K


