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

RNA-seq03:21

RNA-seq

9.9K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.9K
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

13.6K
Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
13.6K
Experimental RNAi02:15

Experimental RNAi

6.1K
RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
6.1K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

9.9K
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...
9.9K
Ribosome Profiling02:24

Ribosome Profiling

3.5K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.5K

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

MPCLCDA: predicting circRNA-disease associations by using automatically selected meta-path and contrastive learning.

Briefings in bioinformatics·2023
Same author

Apoptosis-inducing effect and structural basis of Polygonatum cyrtonema lectin and chemical modification properties on its mannose-binding sites.

BMB reports·2008
Same author

The catalytic intermediate stabilized by a "down" active site loop for diaminopimelate decarboxylase from Helicobacter pylori. Enzymatic characterization with crystal structure analysis.

The Journal of biological chemistry·2008
Same author

Monitoring prostate thermal therapy with diffusion-weighted MRI.

Magnetic resonance in medicine·2008
Same author

Removal of ammonia nitrogen in wastewater by microwave radiation.

Journal of hazardous materials·2008
Same author

[Three-dimensional anatomical position of rotatory center in cervical rotatory and local manipulation].

Nan fang yi ke da xue xue bao = Journal of Southern Medical University·2008

相关实验视频

Updated: Jun 25, 2025

Author Spotlight: Integrating Organoid Models with Single-Cell and Spatial Transcriptomics Technologies
05:45

Author Spotlight: Integrating Organoid Models with Single-Cell and Spatial Transcriptomics Technologies

Published on: March 29, 2024

2.2K

CVGAE:使用单细胞RNA测序数据进行基因调控网络推理的自我监督生成方法.

Wei Liu1, Zhijie Teng2, Zejun Li3

  • 1School of Computer Science, Xiangtan University, Xiangtan, 411105, China. liuwei@xtu.edu.cn.

Interdisciplinary sciences, computational life sciences
|May 22, 2024
PubMed
概括

我们开发了CVGAE,这是一种自主监督的方法,用于从单细胞RNA测序数据中推断基因调节网络. 它提高了准确性和概括性,甚至在短暂的学习场景中表现优于现有方法.

关键词:
基因调节网络推断推断的基因调节网络推断图形神经网络是一个神经网络.代表性的学习学习.单细胞RNA测序的一个细胞.

更多相关视频

Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells
11:26

Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells

Published on: May 22, 2017

13.8K
High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

10.2K

相关实验视频

Last Updated: Jun 25, 2025

Author Spotlight: Integrating Organoid Models with Single-Cell and Spatial Transcriptomics Technologies
05:45

Author Spotlight: Integrating Organoid Models with Single-Cell and Spatial Transcriptomics Technologies

Published on: March 29, 2024

2.2K
Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells
11:26

Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells

Published on: May 22, 2017

13.8K
High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

10.2K

科学领域:

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

背景情况:

  • 基因调节网络 (GRN) 的推断对于理解基因调节至关重要.
  • 当前的计算方法与高维的单细胞RNA测序数据 (scRNAseq) 和网络稀疏性作斗争,限制了准确性和概括性.
  • 由于这些挑战,现有的GRN推断技术往往产生不满意的结果.

研究的目的:

  • 提出一种新的自我监督方法,CVGAE,用于从scRNAseq数据中准确和可概括的GRN推断.
  • 解决现有方法在处理高维数据和网络稀疏性方面的局限性.
  • 评估CVGAE的表现和学习能力,包括其在少数射击学习环境中的有效性.

主要方法:

  • 开发了CVGAE,一种自主监督的方法,利用图形神经网络进行诱导性表示学习.
  • 整合基因表达数据和观察到的拓到一个低维向量空间.
  • 采用FastICA来降低计算复杂性和多堆叠的GraphSAGE层,并使用改进的解码器来处理网络稀疏性.

主要成果:

  • 与现有方法相比,CVGAE在已知基准真相网络的多个单细胞数据集上表现出更高的性能.
  • 该方法在短暂的学习场景中取得了可比或优异的结果,验证了其学习和概括能力.
  • 来自CVGAE的低维向量有效地根据数学距离预测基因相互作用.

结论:

  • CVGAE提供了一种强大而有效的方法,用于使用单细胞RNA测序数据进行基因调控网络推断.
  • 自主监督,基于图形神经网络的方法克服了以前技术的关键局限性,特别是数据复杂性和稀疏性.
  • 即使训练数据有限,CVGAE对我们对基因调节机制的理解有很大的前景.