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相关概念视频

CRISPR01:59

CRISPR

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Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced...
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CRISPR and crRNAs02:53

CRISPR and crRNAs

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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
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CRISPR/Cas9 Genome Editing01:28

CRISPR/Cas9 Genome Editing

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The CRISPR-Cas system serves as a bacterial defense mechanism against invading genetic elements such as viruses and plasmids, forming the foundation for its adaptation as a powerful genome-editing tool. Originally discovered in prokaryotes, this system has been repurposed to revolutionize genetic engineering across a wide range of organisms, including plants, animals, and humans. The core component, Cas9, is an endonuclease derived from Streptococcus pyogenes, capable of introducing...
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Homologous Recombination02:31

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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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Updated: Sep 19, 2025

CIRCLE-Seq for Interrogation of Off-Target Gene Editing
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CIRCLE-Seq for Interrogation of Off-Target Gene Editing

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基于深度学习的CRISPR/Cas目标外预测模型

Mingming Cao1, Alexander Brennan2, Ciaran M Lee2

  • 1Department of Bioengineering, Rice University, Houston, TX, 77030, USA.

Small methods
|June 5, 2025
PubMed
概括
此摘要是机器生成的。

深度学习模型显示出预测CRISPR/Cas基因组编辑目标外部位 (OTS) 的前景. 整合经过验证的OTS数据可以提高模型性能和稳定性,从而实现更安全的基因编辑应用.

关键词:
这就是CRISPR/CasPR.深度学习模型深度学习模型基因编辑 基因编辑目标网站之外的网站

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科学领域:

  • 基因组学就是基因组学.
  • 生物信息学是一种生物信息学.
  • 计算生物学 计算生物学

背景情况:

  • 克里斯普尔/卡斯基因组编辑提供了精确的基因改造,但面临着非目标效应 (OTS) 的挑战.
  • 准确预测OTS对于CRISPR/Cas技术的安全临床应用至关重要.
  • 在 silico 方法,特别是深度学习,正在成为 OTS 预测的强大工具,因为它们能够学习复杂的序列特征.

研究的目的:

  • 审查现有的目标外站 (OTS) 预测工具,重点关注深度学习方法.
  • 描述用于训练和测试OTS预测深度学习模型的数据集.
  • 评估和比较六个突出的深度学习模型的CRISPR/Cas OTS预测的性能.

主要方法:

  • 审查了当前的OTS预测工具,强调深度学习方法.
  • 用于深度学习模型培训和验证的分析数据集.
  • 通过使用六个公共数据集和CRISPRoffT数据库,评估了六个深度学习模型 (CRISPR-Net,CRISPR-IP,R-CRISPR,CRISPR-M,CrisprDNT,Crispr-SGRU).
  • 使用精度,回忆,F1分数,MCC,AUROC和PRAUC等指标评估模型性能.

主要成果:

  • 深度学习模型显示了预测非目标CRISPR/Cas位点的潜力.
  • 将验证的OTS数据集纳入培训中显著提高了模型性能和预测稳定性,特别是在不平衡的数据集中.
  • 在各种评估场景中,CRISPR-Net,R-CRISPR和Crispr-SGRU的整体表现强.
  • 没有一个单一的模型在所有测试条件下始终超过所有其他模型.

结论:

  • 高质量,经过验证的目标外站点数据对于提高基于深度学习的预测的准确性和可靠性至关重要.
  • 先进的深度学习架构,当与适当的数据进行训练时,可以显著提高CRISPR/Cas目标外站点的预测.
  • 整合强大的预测工具对于确保CRISPR/Cas基因组编辑在临床环境中的安全性和有效性至关重要.