Jove
Visualize
联系我们
JoVE
x logofacebook logolinkedin logoyoutube logo
关于 JoVE
概览领导团队博客JoVE 帮助中心
作者
出版流程编辑委员会范围与政策同行评审常见问题投稿
图书馆员
用户评价订阅访问资源图书馆顾问委员会常见问题
研究
JoVE JournalMethods CollectionsJoVE Encyclopedia of Experiments存档
教育
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab Manual教师资源中心教师网站
使用条款与条件
隐私政策
政策

相关概念视频

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

10.2K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
10.2K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.0K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
18.0K
Epistasis Analysis01:09

Epistasis Analysis

5.3K
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
5.3K
Variability: Analysis01:11

Variability: Analysis

192
Measures of variability are statistical metrics that reveal the dispersion pattern within a dataset. They are pivotal in biostatistics, providing insights into the heterogeneity within health and biological data. Variability signifies the degree to which data points diverge from one another, helping researchers understand the potential range of values and associated uncertainty within the data.
The range is a simple measure of variability, indicating the difference between the highest and...
192
Neural Regulation01:37

Neural Regulation

40.4K
Digestion begins with a cephalic phase that prepares the digestive system to receive food. When our brain processes visual or olfactory information about food, it triggers impulses in the cranial nerves innervating the salivary glands and stomach to prepare for food.
40.4K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.2K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.2K

您也可能阅读

相关文章

通过共同作者、期刊和引用图与本文相关的文章。

排序
Same author

Using Deep Learning Models of Gene Regulation to Guide Drug Prioritization.

bioRxiv : the preprint server for biology·2026
Same author

Regulatory risk loci link disrupted androgen response to the pathophysiology of polycystic ovary syndrome.

Journal of the Endocrine Society·2026
Same author

Enhancing Long-Term Care Efficiency: Embedded LLMs for Clinical Report Summarization and Caregiver Support.

AMIA ... Annual Symposium proceedings. AMIA Symposium·2026
Same author

Silencer variants are key drivers of gene up-regulation in Alzheimer's disease.

Science advances·2026
Same author

Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants.

Genes·2025
Same author

Super-silencers are crucial for development and carcinogenesis in B cells.

Nature communications·2025

相关实验视频

Updated: Sep 18, 2025

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

535

对深度学习模型进行比较分析,以预测因果监管变异.

Gaetano Manzo1, Kathryn Borkowski1,2, Ivan Ovcharenko1

  • 1Computational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, USA.

bioRxiv : the preprint server for biology
|June 26, 2025
PubMed
概括

卷积神经网络 (CNN) 模型擅长预测基因变异对增强剂活性的影响. 混合CNN-变压器模型最适合在链接不平衡块内识别因果单核酸多态 (SNP).

科学领域:

  • 基因组学就是基因组学.
  • 计算生物学 计算生物学
  • 分子生物学分子生物学

背景情况:

  • 全基因组关联研究 (GWAS) 识别与疾病相关的非编码变异.
  • 区分因果变异与关联是非常具有挑战性的.
  • 深度学习模型预测遗传变异的监管效应.

研究的目的:

  • 评估最先进的深度学习模型,以预测基因变异对增强器活性的影响.
  • 在不同的模型架构和数据集中比较性能.
  • 确定最佳模型来预测变量效应.

主要方法:

  • 评估了来自MPRA,raQTL和eQTL实验的9个数据集.
  • 在四个人类细胞系中评估了54,859个单核酸多态 (SNP).
  • 将卷积神经网络 (CNN),变压器和混合模型进行比较.

主要成果:

  • 在预测SNP监管影响方面,CNN模型 (TREDNet,SEI) 始终优于其他模型.
  • 混合CNN变压器模型 (Borzoi) 在识别链接不平衡块内的因果SNP方面表现优异.
  • 微调改进了变压器模型,但没有超过CNN或混合模型.

更多相关视频

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
07:15

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Published on: January 16, 2019

11.1K
Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers
03:37

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

919

相关实验视频

Last Updated: Sep 18, 2025

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

535
Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
07:15

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation

Published on: January 16, 2019

11.1K
Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers
03:37

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

919

结论:

  • 在预测基因变异对增强剂的监管影响方面,CNN非常有效.
  • 混合模型在复杂的基因组区域中精确定位因果变异方面具有优势.
  • 为了在基因组学中进行强大的深度学习模型评估,需要标准化的基准.