利用CIRI3在太字节规模的RNA-seq数据集中检测和定量环状rna。

IF 41.7 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Nature biotechnology Pub Date : 2025-10-01 DOI:10.1038/s41587-025-02835-1

Xin Zheng,Jinyang Zhang,Lipu Song,Xiang Jennie Li,Fangqing Zhao,Yuan Gao

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引用次数: 0

摘要

为了解决环状RNA （circRNA）分析中的最新挑战，我们提出了CIRI3，一种用于在太字节规模的RNA测序数据集中检测和定量环状RNA的工具。CIRI3使用动态多线程任务分区和结点读取的阻塞搜索策略，比现有工具快了一个数量级，同时提供了更高的准确性。我们在2535个癌症相关样本中发现了不同剪接的环状rna，并构建了一个预训练模型和一个生物标志物网络，作为CIRIonco数据库。

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Detecting and quantifying circular RNAs in terabyte-scale RNA-seq datasets with CIRI3.

To address recent challenges in circular RNA (circRNA) analysis, we present CIRI3, a tool for circRNA detection and quantification in terabyte-scale RNA-sequencing datasets. Using dynamic multithreaded task partitioning and a blocking search strategy for junction reads, CIRI3 is an order of magnitude faster than existing tools, while providing increased accuracy. We identified differentially spliced circRNAs across 2,535 cancer-related samples, and constructed a pretraining model and a biomarker network provided as the CIRIonco database.

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来源期刊

Nature biotechnology 工程技术-生物工程与应用微生物

CiteScore

63.00

自引率

1.70%

发文量

382

审稿时长

3 months

期刊介绍： Nature Biotechnology is a monthly journal that focuses on the science and business of biotechnology. It covers a wide range of topics including technology/methodology advancements in the biological, biomedical, agricultural, and environmental sciences. The journal also explores the commercial, political, ethical, legal, and societal aspects of this research. The journal serves researchers by providing peer-reviewed research papers in the field of biotechnology. It also serves the business community by delivering news about research developments. This approach ensures that both the scientific and business communities are well-informed and able to stay up-to-date on the latest advancements and opportunities in the field. Some key areas of interest in which the journal actively seeks research papers include molecular engineering of nucleic acids and proteins, molecular therapy, large-scale biology, computational biology, regenerative medicine, imaging technology, analytical biotechnology, applied immunology, food and agricultural biotechnology, and environmental biotechnology. In summary, Nature Biotechnology is a comprehensive journal that covers both the scientific and business aspects of biotechnology. It strives to provide researchers with valuable research papers and news while also delivering important scientific advancements to the business community.