EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Genome Biology Pub Date : 2024-12-18 DOI:10.1186/s13059-024-03449-7
Zijing Gao, Qiao Liu, Wanwen Zeng, Rui Jiang, Wing Hung Wong
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Abstract

The inherent similarities between natural language and biological sequences have inspired the use of large language models in genomics, but current models struggle to incorporate chromatin interactions or predict in unseen cellular contexts. To address this, we propose EpiGePT, a transformer-based model designed for predicting context-specific human epigenomic signals. By incorporating transcription factor activities and 3D genome interactions, EpiGePT outperforms existing methods in epigenomic signal prediction tasks, especially in cell-type-specific long-range interaction predictions and genetic variant impacts, advancing our understanding of gene regulation. A free online prediction service is available at http://health.tsinghua.edu.cn/epigept .
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EpiGePT:一个预先训练的基于转换器的语言模型,用于情境特定的人类表观基因组学
自然语言和生物序列之间的内在相似性激发了基因组学中大型语言模型的使用,但目前的模型难以纳入染色质相互作用或预测不可见的细胞环境。为了解决这个问题,我们提出了EpiGePT,这是一个基于转换器的模型,旨在预测特定环境的人类表观基因组信号。通过结合转录因子活性和3D基因组相互作用,EpiGePT在表观基因组信号预测任务中优于现有方法,特别是在细胞类型特异性的远程相互作用预测和遗传变异影响方面,促进了我们对基因调控的理解。一个免费的在线预测服务可以在http://health.tsinghua.edu.cn/epigept上找到。
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来源期刊
Genome Biology
Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍: Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.
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