ViTrace使用混合语言模型检测瘤转录组中的病毒特征
Feng Zhou1,2, Yushuang He2, Fan Yang2
1National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, China.
Communications biology
|December 14, 2025
概括
ViTrace使用一种新的语言模型在瘤RNA中识别病毒,改进了癌症研究. 这个工具可以检测出已知的和新的病毒,帮助精确的瘤学和理解病毒与癌症的联系.
科学领域:
- 在瘤学瘤学.
- 病毒学 病毒学
- 生物信息学是一种生物信息学.
背景情况:
- 在瘤转录组中识别病毒对于理解瘤发生和瘤进展至关重要.
- 目前使用序列对齐的病毒识别工具与病毒突变,分歧和不完整的基因组作斗争.
研究的目的:
- 开发ViTrace,一种新的混合语言表示学习模型,用于检测人类转录基因数据中的病毒序列.
- 评估ViTrace在不同,以前未见的病毒菌株上的表现及其在癌症研究中的应用.
主要方法:
- ViTrace集成了DNA上下文,位置关系和氨基酸编码信息.
- 该模型在有限的病毒物种上进行了训练,但在广泛的缺席病毒中进行了测试.
- 应用于从食道和口腔膜状细胞癌中获得的单细胞RNA-seq数据.
主要成果:
- 在1179个不在列车中的病毒菌株中,ViTrace在935个物种和167个属中实现了86.39%的召回.
- 该模型揭示了癌症数据中的瘤,细胞和患者特定的病毒殖民模式.
- 在分析的癌症类型中发现了已知和以前未报告的病毒.
结论:
- ViTrace提供了一个可扩展的框架,用于在转录基因数据中检测病毒.
- 该工具通过识别与瘤相关的病毒来促进精确瘤学.
- ViTrace有助于发现新型,未经表征的瘤相关病毒.
相关概念视频
Hybridoma Technology
17.1K
Hybridoma technology is used for the large-scale production of monoclonal antibodies. Monoclonal antibodies bind to only a single antigenic determinant or epitope. Such antibodies are used in research, diagnostics, and disease therapy. The hybridoma technology established in 1975 by Georges Köhler and Cesar Milstein was awarded the Nobel Prize in Medicine in 1984 for revolutionizing research and therapy.
Hybridoma Selection
Commonly used fusion techniques — electroporation,...
Hybridoma Selection
Commonly used fusion techniques — electroporation,...
17.1K
Improving Translational Accuracy
14.0K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
14.0K
Improving Translational Accuracy
3.5K
3.5K
Leaky Scanning
5.6K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.6K
Viruses with RNA Genomes
698
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...
698


